I ended up restarting my campaign as it was still in early game. This time I paid up and got on the pope's good books to avoid the excommunication. It won't last though as unifying Italy will involve going to war with the Papal States sooner or later. But by then I'll either control the curia or be in a position where the excommunication won't matter as much.
Always meant to try EUIV.
I own almost every paradox game with full dlc... it's kind of a problem because I have only put proper time into a few of them.