I will try weigh in with some of my thoughts behind all of this. Note that I am not saying that the points made by others here are not perfectly valid - I am just trying to add other perspectives to the debate.
I think Alisa and Windemere presented the SCoP alignment and relationships with others fairly well.
For me it is very amusing, personally, to hear the debate that EC should be goodaligned. Either as part of making sure the "good aligned" side should have a caster option or because it is the players in the guild, the theme fits better, or because they are connected with a good aligned guild.
SCoP opened and people learned it was good (oh the horror!) I found that people took a major offense, the Elementals are neutral - good vs evil has no place in that guild, it should only be about worshipping the elementals full time, and the whole anti-undead stuff had no place in Calia - and now here we are debating whether or not the more neutral aspect of the Elemental guilds should be good-aligned?
As for the whole Academics should not be in Calia because the Academics are then associated with the Calians, SCoP or EW. Well I think the Academics fit nicely in Gelan and I see no reason why the Academics cannot be evil - many Cadets are quite often. If anyone finds it is a great and terrible wrong, I think there are newbies and room enough upstairs for anyone to "wiz and do it yourself"

All the real (I think) newbie Academics I have met have all praised the guild, the theme and the setup so maybe it is not the calamity we think it is?
If I were to present some of my thoughts (and believe it or not - this is the short version of this note) on the EC and alignment.. I would like to establish a baseline first:
Baseline / this note
My conclusions are based on my personal assumptions and my viewpoints/ontology. It is very possible I am biased and so you can freely critisice both my rationale and my objectivity. Also be sure to split Hektors and my viewpoints apart (He and I sometimes disagree on the subject - for natural reasons he is a bit more biased than me).
I am not at all trying to be objective, nor am I trying to rationally convince anyone here about anything.
This note is only about adding my perspective and firsthand experience in a somewhat analytical manner. So if you believe I am biased and this is all propaganda, fine, as always - have your source critizism well at hand and leave it at that. In other words: I will of course be glad to expand on my viewpoints but juvenility and personal attacks I do not spend my free time on

A few basic assumptions.
Yes the alignment system is flawed. It still helps provide some guidelines for RP and promotes conflicts. These two things help the game tremendously.
When I read the Calian Chronicles, the Calian helpfiles and the underlying theme of the Calian Warriors I believe there are plenty aspects in Calias history, the history of Caliana, the Warriors, their viewpoints, how they persue their goals etc to support them being good aligned.
They may not be as diehard honorable and full of justice as the Knights or as direct and partial towards evil as the Rangers or etc etc but they are a good aligned guild in the core.
The Calians can easily be good aligned and work together with a neutral cleric guild if that guild does not do something that is in strong violation of the Calian principles.
There have been examples of alignment-based guilds and neutral guilds working together before.
Having read through the arguments presented in the thread, along with the various debates I have had with players over the years I will try to build the note as follows:
Note buildup.
1. SCoP is one of the sources of the guild.
SCoP is good aligned
SCoP is good by association
Anti undead theme and alignment
2. EW is another source of the guild.
The EW is neutral
3. General good vs evil magic in Genesis
SCoP closes - EC opens as neutral
4. The players in the guild
Ad 1. SCoP is goodaligned
SCoP has two themes it draws alignment from.
The Elementals are neutral. They can be interpreted as supernatural beings, forces of nature, raw elemental energy, gods from the elemental realm - etc etc. They are neutral.
The ancestry is strongly good aligned. I will not go too much into it, as discovering the arguments and spending time on exploring Calia to learn this is part of the SCoP application process. Just accept that for the sake of the argument that there is heavy argument on why SCoP can be goodaligned.
SCoP is mostly good and partially neutral in this perspective.
SCoP is good by association
SCoP has taken whatever help it could find yet also has an ancestral dislike for invaders. The SCoP is part of the Coalition with the Warriors to protect the Sanctity of their greater work and their temple. If the BDA, RDA, Mercenaries, Shadow Union or whichever had offered to help protect the Temple and Calia I am fairly certain the SCoP would have said thank you very much.
SCoP tried to get form an alliance with the Calian Warriors a few times but with past inactive councils and the general dislike (naturally) of having vampires and/or morgul mages as enemies has made it hard for SCoP to find allies anywhere

SCoP was not exactly welcome in the Alliance of Elnoven (closed Mystics, Knights, Rangers, Calians) or in the New Alliance. (Neidar, Rangers, Calians, Knights). No complaints there - RP wise SCoP are very stand alone or and I certainly understand why those guilds did not want to hear Hektor huffing, puffing, complaining and berating them all the time or for that matter have the Vamps fangs in their necks:) (whichever horror is the worst I am not always sure!).
The SCoP was in cooperation/allied with PoT and BDA at a time. That could happen again if it made sense. Does that make SCoP evil? The SCoP was at a point in debate with some of the Dragon Orderleys about an alliance? Does that make SCoP neutral? I do not think so.
Right now SCoP are in cooperation with the Calian Warriors.
It is true that the Calian Warriors and the SCoP has an associated history, but so does the Rangers, the Thornlin Milita and the Heralds of the Valar. These guilds have their alignment not because of their history together but because the wizards who created the guilds felt that alignment fit the theme of the guild - not because the players later decided to find alliances in whatever other guilds or not.
The Morgul Mages and the Shadow Union were strongly allied for a time longer than the SCoP has ever been allied with anything. I do not think anyone ever considered the Shadow Union should be recoded into an evil guild for that alliance.
(of course, the whole worshipping demons and upholding a pact of tyranny with them in a system of race segregation and castes with slavery could be considered very lawful evil and impact SUs coming recode, but thats another story entirely).
In short.
SCoP is NOT good by association. Given the SCoP is good and the enemies often are evil they of course has an easier time finding allies among the goodaligned guilds.
SCoP is mainly neutral in this perspective.
Life&death vs undeath.
Again, not wanting to spoil too much for applicants- SCoP has a strong anti-undead side (both thematically and hard coded) that can argue in favor of both good alignment and also neutral alignment. After all - the only good undead is a "dead?" undead but also what life and actions often leads to undeath (ones own or others)?
SCoP is mainly neutral in this perspective.
Subconclusion 1
So in short, if we argue that SCoP is one of the sources of the new EC guild then yes the EC could be good aligned. They have the same ancestry and serve neutral elemental gods. They would also have an easier time finding friends in the good aligned guilds as they will (as the worshippers (hard coded antiundead) and the spirit circle (thematic and hardcoded anti undead) did) have friends in the guilds opposed to the undead (often good aligned - feel free to code some evil undead hunters and see how quickly Hektor can compromize for the greater good or well neutral:)).
SCoP as a source can push the alignment to either side.
Ad.2. EW is also a source of the new guild
The EW has always been neutral. As I have understood (from the wizards) it that was because there needed to be neutral layman options (not many at the time) as well as the gods being neutral. It was built on the remains of the Hellfire club and not meant to replace the mystics directly but add some of the same RP concepts to Genesis.
The EW has an approach and the that can support any alignment and its inner unity is above alignment. (which sometimes makes it very hard for certain guilds to join because they have a greater calling towards a more uncompromizing unity).
All alignments can join EW. The guild had, hase and will have BDA, RDA, AA, evil monks etc etc members.
Ok Ill bite and waste my time on a little bit of the juvenile posting.
I believe Draugor was a member, while some of these guildmembers joined and I don't recall Draugor being much of a buttbudy to anyone in his joining?
One of the application tasks relate directly to respecting all guildmembers regardless of occupation. So hands of the trolling propaganda machine and post some actual constructive critizism and helpful input, Draugor?

Back in 98/99 The Walkers opened. It was the first occupational elemental caster guild. They were "Avatars of the Elementals"/"Seekers of the raw Elemental powers" based. Loremasters (mages/mystics)/ (seeekers) who devoted themselves to the gods (clerics)/(seekers) to gain insight and power to defeat the "Ancient Enemy" (the "thing" behind Kroug and the undeads in Calia (and yes there were undeads in Calia at that time too and more planned - the wizard just never got around to it)).
It is true that this guild had a derivative from and a strong and very respectful nod towards the Mystics. To say the EW/Walkers/SCoP/EC has completely derailed from that would require a better understanding of the Mystics than mine and I think partially moot to the point of what the guild will be in the future
The Walkers were closely tied with the Worshippers (occupational branches of the guild) and neutral aligned as well.
In essence it has always been the idea that these guilds could be neutral if they were devoted strongly to the gods. The SCoP differentiated in being closely tied with the ancestry of the lands as well.
EW as a source mainly pushes the alignment towards neutral.
Subconclusion 2
The EC can be both good and neutral, but certainly leans strongly towards the neutral side.
However, it would require that we rework the theme of the layman, and some layman members would have to be kicked out due to the alignment demands.
Ad 3. General alignment and caster options in Genesis.
It has been stated, I think sometimes by Snowroses player lately that when SCoP closes and EC opens as a neutral guild then there will be no good aligned caster guilds left.
It is true that the Rangers have useful spellcasting abilities, but they are apart from being the Rangers of the Westelands also coded as a "ranger style" guild. They draw both from fighting abilities (such as brawling etc) and spellcasting. I agree they are not an equivilant to the SCoP, Mages or PoT.
One of the reasons, I believe, without knowing it for certain that SCoP is good aligned was also to make sure there wouldnt suddenly be three evil caster guilds in effect. It is also an issue, I think that for players who want to be casters that they would either be undead mage/clerics or evil clerics. Some would want to be neutral, others good.
In the whole "evil guilds vs good guilds" debacle in the case of SCoP or ECs it would not make a major difference but in impression. It has more to to do with character options for my part.
Subconclusion 3
The lack of a goodaligned caster options speaks in favor of making EC good aligned. However, anyone can be a good or evil Cleric in the new guild. I do not think that is possible in PoT or MM? (I dont know!).
The need for a good aligned caster guild suggests a need for the EC to be goodaligned, and it could work since it is derived from SCoP and currently the only actual option (that I am aware of) to a good aligned caster guild.
Ad 4. The players.
I do not know who will be "the players" in the new EC guild. All I do know is that SCoP will close/merge into EC and the Clerics in SCoP will be offered some sort of a transfer. What that will mean I do not know.
The players in SCoP so far I believe have all handled quite well the balance between having both a neutral and good-aligned core. I have no doubt they too would manage that in a neutral guild. To suggest otherwise is, as Alisa puts it critzism of the players not the theme of the guild.
Subconclusion 4
This point could suggest the players are incapable of handling roleplay.
It is irrelevant in the setup of the theme of the guild.
Conclusively
While there are many factors that suggests the guild must be neutral you can also find premise for it being a goodaligned guild. Essentially I believe it should be neutral with room for all the internal challenges, guild relations and opportunities that have which is (pun intended) quite in alignment with the concept of the guild, the domain and the original intent of the creators.
However, all in all, it is up to the wizards to decide and I can certainly understand the arguments presented by others here.
So what does everyone think? Would you rather see the the EW made selectively good aligned and the EC developed a more "goodie goodie two shoes Cleric" than the current somehwat distant "care for all Creation and the continuity of life and death, no matter the direction it takes."
I am strongly in favor of the latter.
Cheers