It's possible to get banned from attacking more than one faction in one go. It all depends on your favour with him. Keep bribing the Pope and he'll shut up for a while.

Other than that, I can only say that it takes patience.

If his favour is high with you (8-10 cross), he'll send you a stop order after a few turns of aggression. If it pops up while your besieging you can proceed to assault the castle without risk of excomm. You'll fail the mission but take only a small rep loss.