Domains, Spells, etc
I guess the first thing to do is decide the 'truth' of the universe you're making, Since we're dealing with the Crusades and my notion of history is faulty, I might be a century or two to far one way or another with some ideas
1. Find out what stage the Bible was at, at the time you're setting this. If I remember right, the Bible we normally use today is still being assembled until it's closed at one of the large meetings (sometime in the 1500's?). Revelations might not be in there, along with some other things that haven't been taken out.
2. Read up on the Prodestant Reformation, since that'll tell you what Luther took out.
3. One post above mentions that early Judiasm took some time to go completely monotheistic: other gods might actually exist, but just be 'banned'm, depending on the version of 'truth' you want for the game.
4. Remember the Niphelim, the 'Giants in the Earth'. They're still around, since they also survived the Flood by unknown means. They might be a path to magical power of a 'Godly' nature.
Assuming we want Christian Magic of a type, the next thing to do is decide on the power level. If you want the standard D&D power level, with spells, domains, all the rest, then I think you could just go with God (Good, Law, Sun, Air, Travel) and Satan (Choas, Evil, trickery, Destruction, and Death) domain lists.
If you want a more 'historical' magic system, do everything with Feats and Granted Powers. A cleric of God could use a lot of the weird new Extra Turning-powered Feats in
Defenders of the Faith then every other level gain some kind of granted power, but no actual 'spells' with the possible exceptions of the 0-level spells and the Healing stuff.
For the Disloyal Opposition, use the Witch class in the DMG with it's mix of Arcane and Divine spells. Demons, devils, spirits, etc, can be bargained with by the summoner (usually with disasterous consequenses).
You might want to look at the Ars Magica system (latest edition) for ideas as well.