Who Would Win?
Who would win? In a war, no one truly wins, do they? But that's no fun.
Of course everyone must realize too many unspoken factors, not to mention just plain old dumb luck, will probably tell more than all the analysis one can bring to bear on the problem. But that's no fun.
On the morality front, I don't think it's a must the magocracy be evil or even neutral. Two LG forces may easily oppose one another given the right circumstances. I'd certainly say the theocracy would lose, however, unless we further assume they are monotheistic and not polytheistic, as is the case in most D&D games. No one bickers or argues or hates each more than competing religions. Even two LG factions would likely not work so well together.
I would tend to think the magocracy would win. It's more mobile, it quick, the damage is larger, and greater mobile offense usually is superior to greater fixed defense, which the clerics would have. Still, the true power aside from sheer numbers found in the masses has to come from individual high level adventurers.
Wizards are excellent at hit and run tactics while clerics must be more stationary if their healing powers are to be fully utilized. If they aren't right there, it'll be too late for healing, so you have to know where they are. I think they would have to operate more like M.A.S.H. units in large scale operations. But the power of the church is too localized in temples (I admit I'm assuming temples are actually important). What happens when wizards take them out? Essentially nothing, or quite a bit? It's difficult to assess the true military value of such locations. Wizard, on the other hand, can probably do more magic in more areas. Anywhere, anytime, that's their motto.
The Enlarge spell will probably tell the tale. One 1st level kamikaze mage brought in with a higher level mage by teleportation, left behind with a small quantity of Uranium 235, casting Enlarge on it after the higher level mage leaves, ought to do it
Pretty good for a 1st level spell. But that's no fun, and I'm sure many people are retching at the very suggestion (so you should know, I'm not seriously suggesting this should happen).
Still, unless we assume the gods merely offer normal support, as represented by normal spells given to their clerics, and not take a more active hand, we can't really have the theocracy losing. But it's not really gods vs mages here, which is no fun, so we won't assume the gods take an active hand. But never discount the power of divination spells like commune. Are they there? No. Are they there? Yes. Ah HA!!! Talk about great Intel.
Healing is all very well and good, but you can't spread it around fast enough. At best, it serves well to patch up the seriously wounded who would have otherwise died, even then only enough is used to keep them alive, and natural healing is left for the rest. It's important such spells be reserved for those worthy select few high level types to keep them in play, while grunts will fall by the thousads never seeing any help from healing magic. It's always been easier to destroy and harm than heal and build, so the magocracy isn't really too seroiusly out classed here.
Can both sides equally summon creatures that need magic weapons to even hit them? Whoever can do that better has a huge advantage, but I'm not sufficiently familiar with 3e yet to know who can do it better there.
Ultimately, however, I must favor intelligence for its logistics, mages for their mobility and damage, and discount clerics as their skills are more suited for support, healing, and building which will never be faster than the mages attacks, harming, and destructive capabilities. The best thing I've heard on the cleric's side is fact their grunts may more willingly go to and die in holy war, which is no biggie if one is assured a sweet spot in the after life. Then again, it isn't really required the magocracy by an atheistic nation where no similar support or propaganda could do as much.
The only certainty I feel is that it will be ugly, and probably quick. The longer it drags on, the more the clerics may somehow regroup, but their holy shrines and temples will no longer help them as they'll be the first things to go, and if they in any way help connect the faithful to god, without it, what chance do they really have?
Jim.