The Pope acts as a counter balance to one catholic faction dominating the others. You can just ignore the Pope and be excommunicated, but that has a lot of negative side effects. Instead, wait for the duration of the Pope's warning to expire (I think you can check it in the missions tab) and build your army. Once it expires attack your opponent at several places at once using siege equipment to break walls. Since you defeat your opponent in a single turn, if the Pope once again warns you not to attack you can just hold in place with your new conquered territories.

Sometimes the Pope's warnings go both way and if your opponent attacks you, they will be excommunicated. This gives you free reins to attack as you see fit.