I don't think religion is a key element of hte mod, to be honest.

In the vanilla game, you have 'christian' and you have 'muslim' and they are naturally oposed to each other. Christian faction attacks christian faction, and the Pope gets annoyed. Crusades and Jihad's are called on the opposite sides territories.

The need for religion to control or influence a city is not relevant to a situation where an entirely different species takes over a city. I can't imagine 'religous unrest' being a factor in an Empire city being overrun by Skaven.....Oooohhh...you refuse to worship the Horned Rat ... oh..thats because we killed and ate you all.