Maybe I'm out of turn, but it seems like this mod is running counter to the philosophy of the game slightly in that it is restricting the religious movements in-game to historical implimentations rather than allowing the "what if something else happened" scenarios. One of the specific quotes from the manual was "what if Judaism developed a missionary tradition?" There's nothing inherint in Judaism per-se that restricted that from happening. It's just the way things worked out.
Maybe another approach to take would be to treat religions as having a primary and secondary characteristic ala the civilizations leaders that adds a positive influence on an aspect of the religion? Christianity might have traits like "evangelical" (more, cheaper missionaries) and "organized", Islam "evangelical" and "ummah" (double foreign leader pleasure for same state religion,
http://en.wikipedia.org/wiki/Ummah), Zoarastrian "philosophical" and "juristic" (decreased maintenance or similar)... etc. You are then not judging a religion as having negatives as much are you are recognizing that the core beliefs of some are given to express themselves in certain ways.
Adding "Atheism" as a religion that is created by the "humanism" advance might also make sense. Actually, it should probably be called "Secularism" or possibly "Positivism" since you shouldn't define something by what it's not. Religions are not necessarily anti-science (
http://en.wikipedia.org/wiki/Islamic_science) but more than others it may have "scientific" (bonus research) and "material" (bonus commercial) as properties. Positivism's temples may be any social structure that highlights humanism. I'd look for a common municiple element of maoist china, communist russia, and their satelites to see what filled this role.
A world event which creates a schism in an established and spread religion would be an awesome addition as well. What if Budhism had split like Islam? Or what if Hinduism split twice like Christianity (Roman v Greek, Catholic v Protestant) resulting in drastic shifts in forgien policy and sparking continential wars and chaos as your income from the adherents was halved. It would be bad, of course. Possibly caused by warring with a nation of the same faith, or by having a civic despised by the religion. (Christianity: Serfdom?, Islam: Caste?, Hindu: Organized Relgion?)
I love the idea of giving religions a greater depth in the game. I think this mod is a step in the right direction, but maybe just a little more to the left.
(Sorry if this came across as a lecture. I mean no offense to the obvious hard work and deep consideration displayed by the mod's creator)