Yep I can see your point especially in relation to breaking down Christianity (reflectings its denominations) and for competitive gameplay too.
In regards to Christians (these are specualtive estimates) there are about 2.2 billion (of which 1.2 are Catholic, about 240 mil are Eastern Orthodox.
Of Muslims, there are about 1.6 billion, I think about 250mil of which are Shia. Interesting in this article,
http://en.wikipedia.org/wiki/Shia_Islam it indicates at least today that Shia represent a distinct minority in most Muslim countries.
Historically we also know that the violence (Between Sunnis and Shias) were such, that its a shame that it can be noted (somehow). I think I would love to see this schism reflected especially as it concerns a great schism in the worlds 2nd largest religion (and fastest growing) then these denomination distinctions may have yet an even larger role to play.
Perhaps the penalties of these differing denominations could be less between the Islamic (or most Islamic leaders?) Some were particularly hardcore against Shias... for example, such as the Ottoman campaigns against the Shia's of Anatolia (not disimilar but smaller in scale to the crusades.)
I think your right in saying that gameplay is the tricky one here to balance, (especially in the face against the wide spread of Christianity in the game) however, later game Islam continues to retain a level of 'unity' that seems a little ahistorical compared to the (brilliant and freakin awseome) attention given to Christianity.
So id implore you to consider a 2nd look, perhaps even with an exploration to alternatives to Shia as a religion/denomination ingame but (perhaps it can trigger an event or something else to reflect its contributions to history.) In anycase keep up the great work - your vision is seeing this through however you decide to go!