Hmmm interesting idea indeed my next step was to place quests into the campaign eg if your a catholic nation a search for the holy grail in the middle of your campaign (a scripted yes no message from the pope compelling you to search for it then scripted random location of it in the middle east where you have to find it crossing muslim land and well that weill cause war LOL.
But yes its possible to add buildings like you mentioned with the option when you capture the city the belong to destroy them ill look into it Might be very interesting i could make them so they give a huge conversion to that religion so another words if your catholic and you leave the muslim building there it will make it hard to run the place as the population will turn muslim but if you destroy it i can put you instantly at war with all the muslims.