If you got the manpower in the city/fortress let them initiate the siege assault and crush them on the walls and/or streets as the defender. If you dont have the manpower try and get reinforcements up next to besieged city/fortress. Alot of times the enemy will back off. Sometimes they wont.

And that notion that you can attack anyone on your own territory free of penalty from the Pope is wrong. He can and will excommunicate if you are the attacker even on your own territory. I've seen it in my games. I dont think its right but I didnt design the game and make the rules. The trick is to get the enemy be the attacker and *you* be the defender. If you are the defender then you dont have to worry about excommunication. At least I havent seen it yet. Ratings might go down but no excommunication anyway.