Oh you and your perfectly reasonable requests.
Hmmm...
Given the number of enemies you'll have running around and multiple tactics (due to multiple factions) I'd limit the terrain down to 2 features. I don't have DMG2 handy so I'm making stuff up based entirely on the description you gave ... Having said that, from your list ....
Doomcrystal is great thematically but won't add much to the story of the encounter. Plus, as you said, the party already has plenty of light. So it'd just be extra bookkeeping for you and not much else....
Likewise, energy nodes would be good, especially in tieing in earlier campaign events. But the other two actually have the strongest story appeal (based on the short synopsis you gave here anyway).
So I'd go with the other two (one giving some sort of benefit to each faction) ...
THIS IS ALL OFF THE TOP OF MY HEAD - I emphasize that to point out I am not giving exceptional consideration to how hard it will be to utilize (you will want to use something -simple-). But I'm sharing these (slightly complex) ideas since they could help inspire you.
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Rubble
Randomly toss in some rumble from the decayed building and it's difficult terrain. (Easy and simple and no real tracking necessary)
Columns
Toss in one or two support columns that are impassable terrain that were once support columns to keep the chamber's ceiling up. (Easy and simple and no real tracking necessary)
Far Realm Portals
Far Realm Horror (Aura 5) * Fear. Any nonabberent creature that ends its turn in the aura is slid 4 squares and cannot end this movement in any Far Realm Horror aura.
Initiative: End of round
Far Realm Transport (At-Will). Standard Action. 1d4+2 Far Realm minions are summoned from each active portal and appear in a square adjacent to the portal. The summoned minions can take one action when summoned and then have their normal turn during the next turn. On subsequent rounds, they act on initiative just before the Far Realm portals.
Disable: When adjacent to a portal, make an Arcana check (DC medium or hard, depending on if you have multiple PCs with high arcana). After 3 successes, that one portal is disabled. A natural 19-20 on Arcana counts as an automatic 3 successes for that portal.
Note 1: You may want to adjust the number of summoned minions depending on the number of portals you finally decide to use.
Note 2: The aura may seem unnecessary, but you'll want -something- there or else you'll have a PC that camps by the portal and just keeps using readied actions to blast the minions as they come through with no real effort. So this will be lots of running up trying to disable it then seeing something inside that scares them away for a moment.
Note 3: the summoned minions should get that one action when summoned as way to help spread them out but don't just move them to the side of the PCs expecting to hit them next turn since the PCs would go next and just kill the minions before they did anything.
Note 4: To cut down on tracking, if your undead faction is immune to fear, you won't have to worry about them getting caught in the aura.
Defiled Altar 6 altars in the chamber that emanate with a feeling of dread and glow like a black light, casting eerie illumination in the room
Black Light: Sheds dim light up to 10 squares
Life to Death (Aura 10): Undead creatures gain +1 attack and resist 5 while in the aura. Multiple auras stack.
Death to Life (Aura 10): Creatures without the undead type take -2 penalty to saves and -5 penalty to surge value while within the aura. Multiple auras stack.
DisableTwo successful religion checks (DC medium or hard?) changes the Defiled Altar into a
Sacred Altar (see below).
Counter Disable When a defiled altar has only one (of two) successful disables, one (specific) person from the undead faction can use a standard action religion check (DC ?maybe set by the success) to undo the success, resetting it back to 0.
Note 1: Yes, I know, multiple auras don't normally stack. Which is why I put them in as an exception to emphasize that this place is harder because there are so many of them.
Note 2: I used 10 squares for the auras. However, if it's a smaller chamber, you may want to reduce it to 5 squares. OR if you have more altars then likeiwse reduce it to aura 5. but, ideally, there will be areas where 1 2 or 3 auras can stack. But 1 aura should be frequent enough with 2 and 3 stacking auras being less frequent. and no more than 3 auras stacking in any given square unless you wanted to really make it hard.
Note 3: You can drop the counter disable thing if it would be too much tracking. I just thought since the undead faction had time to prepare they might have knowledge about the defiled altars and know how to 'repair' them. Alternatively, drop this idea from the altar and instead use it on the portal ?
Sacred Altar The defiled altar seems to crackle with light until it bursts with radiance like a miniature sun
Pelor's Light: Sheds bright light up to 10 squares
Undead Bane (Aura 10): Undead creatures take -1 to attacks, defenses, and saves while in the aura. Multiple auras stack (Or if you think that is going to be too much to track "Undead in the aura gain vulnerable 2 per undead bane aura that they are in")
Pelor's Blessing (Aura 10): Creatures without the undead type gain 5 temporary hit points per Pelor's Blessing aura that they are in at the start of their turn.
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It's a lot less verbose when you trim out all my rambling notes in between. But it might still be a lot to track. So trim it down however you want, I just put in off-the-top of my head ideas for inspiration. Maybe go so far as to make Defiled Altar and Scared Altar exact opposites of one another so that you know if someone is in one of each, they would cancel each other out, thus, less to track.
Anyway, hope it helps (even if just for inspiration).