I dunno, if Juedaism and one of either confusianism or taosism were replaced we could have orthadoxy and later prodistantism, this aught to start more wars in europe at least...
I feel as if simply taking out certain religions to create more diversity within others doesn't really address the main problem: religions in Civ4 are too homogenous and don't allow for differences in theology or 'schisms'.
This next bit might be a bit OT, so you can stop reading here if you like
. I think the main problems of religious homogeneity lies in the fact that there is only one holy city/shrine for each faith, when in the 'real world' there are in fact many competing relgious institutions within a single faith. This shouldn't be to difficult to model, however.
Consider having 3 'shrines' for each religion (for example, christianity could have the temple of the nativity for orthodox, the vatican for catholocism, and perhaps the cathedral of cantebury for protestanism). Each shrine allows that civilization to build orthodox/catholic/protestant cathedrals in cites that have a christian temple. These cathedrals can produce a maximum of 3 happiness: 1 for having christianity as the state religion, 1 for having thier shrine within you empire, and a final happiness for a 'favourite' civic of thiers (eg Org religion for orthodoxy, theocracy for catholicism, pacifism for protestanism). In this way, different religious authorities 'pressure' thier respective civilizations to to adopt different civics, leading to differences between empires within a single religions, and, in due time, religious wars. This concept does rely on the fact differences in civics wil cause antagonism between civilizations, but that isn't hard to mod in and would probably more accurately reflect the 'differences' that real civilizations have found between each other.
Whew! sorry for the OT jaunt...