The MICs vary from faction to faction (though some factions share the same ones (Aedui&Arverni - Seleucia&Ptoleamai - Sweboz&Getai - etc)). You can choose leave them all when you take a settlement, destroy them that aren't useful (also, if you lose the settlement the enemies have to start their military over from scratch), or destroy them all even if you can use them to represent the difficultly of a new town (only if you choose something like that for role-play).

All enemy temples will upgrade to a type of temple you have. You can tear them down and build your own temples from scratch or upgrade their temple and just deal with what god it happens to be dedicated to now. I will usually leave advanced temples intact and then choose on a case to case method for all lower temples (if I like the diety they upgrade to).