I think that there should be incentives for the civs to play more according to their lore, but without totally restricting alternative options. So, discuss how the game can be changed to achieve that goal (with strategical considerations being secondary to the lore ones).
1) Make Priests/Eidolons/Paladins abandon you with alignment shift .
2) Make the Elohim unable to build other civ's palaces. Also, make their Tolerant trait not apply to the Infernals.
3) Make Devouts and Lightbringers upgrade only to priests/high priests of non-evil religions.
4) Penalties to the Elohim for high Armageddon count. A sorta reverse Stigmata promotion, perhaps?
Any other ideas?
In addition to making units abandon you based on alignment, I'd limit which priests can upgrade to Eidolons/Paladins/Druids. The extreme alignments could get an extra upgrade. In my version, I usually do it this way:
Confessor -> Prior or Paladin
or Knight
Vicar -> Luridus or Paladin or Druid (Note: I'm not a big fan of any Empyrean priest names, and may change them)
Stonewarden -> Runekeeper or Paladin or Druid
Cultist -> Speaker or Druid or Eidolon
(Shadow -> Eidolon that keeps its invisibility and marksman, Horse Archer -> Shadowrider)
Ritualist -> Profane or Eidolon
or Archmage
The Tolerant Trait has already been blocked from letting you build other civs' palaces, so the first half of #2 is covered.
Frankly, I see no reason why the Elohim should have the Tolerant Trait. It would thematically fit the Kuriotates or Grigori better. FF's Conqueror Trait for Decius is a better use of the assimilation code.
It could be interesting if the Mercurians had something like the Tolerant/Conqueror code that made the mortals of their empire keep the abilities of the civ that summoned them.
According to the lore, Lightbringers were the Malakim holy men whom Varn Gossam united and taught to worship Lugus. Although the Empyrean was not technically founded as an organized religion until Varn's vision at the Mirror of Heaven revealed its central dogmas, Lightbringers were Priests of Lugus since their inception and so should really only be tied to the Empyrean. I don't like Lightbringers being a seperate unit that can upgrade to a disciple of any religion. I think they should be an Ecclesiatic or Vicar UU, maybe with access to Sun Magic in addition to the usual priestly abilities. Sticking closer to the lore, their real strength lies in Divination. I'd like to allow them to perform aircraft-like recon missions (without the animations showing them flying), but it seems allowing lands units to do so will require some SDK changes.
Devouts should be limited to good/neutral religions. Also, I'd probably either move them from Poisons to Way of the Wise or give them an ability to cure poisoned units.
I don't really like giving the Elohim an AC weakness.
One thing I would recommend is to get rid of the hell terrain mechanism that depends on alignment. I like making it so that hell recedes faster from good lands, but can still spread there regardless of AC. I often make hell not spread every turn, but have a random chance based on the AC. Hell terrain can also be more actively spread by making certain promotions (such as Demon, Stigmata, Unholy Taint, and Entropy III) raise the plot counters of their tiles. An evil army will spread hell in its path, even in good lands. I also like making the strongest demons much stronger, but making all non-hell terrains impassible for them. The Infernals would need to corrupt the world before they can conquer it. Since Hyborem is not fallen like Basium, he is limited to following the letter of the Compact, even as he tramples on its intent. He is cannot touch the righteous, at least unless the righteous put themselves at risk by dwelling among the wicked.
The Elohim should not have access to Berserkers. Rage is the Antitheses of the Sirona. Rather than make the Rage technology useless, I'd prefer to give them a unit that uses the understanding of anger to help disturbed find peace. I call this Berserker UU the Paraclete, although I'm not fully sold on the name. It is a Monk upgrade with lower strength, Spirit affinity (Spirit is made to do Holy Damage), the ability to target/defend first against Ira, Odio, Chaos Marauders, and the Avatar of Wrath, and a bonus against each unit. It has a spell that can remove Crazed, Enraged, and Burning Blood from any unit nearby, regardless of who owns it.
Sometimes I give the Bannor a Patriarch as a Prior UU. The exact difference between the 2 units may vary. I usually move Unyielding Order from Order/Divine/Channeling 3 to Law 3, and give Priors a new spell. Sometimes their new spell is Pillar of Fire (removed from Chalid, as the Empyrean is too militant and in the lore it was high priests of Junil who tied using this against the Luonnatar), sometimes a new
Banish spell to be used against demons (it may kill, immobilize, make the target run away, or transport it back to the owner's capital). If I give one one to Priors I may yet Patriarchs use both. Alternately, I might make Patriarchs be Priors with Law III. Sometimes I'll bring back the old Holy War effect and let Bannor Patriarchs force other Order civs to join their crusades.