There's a difference between being excommunicated and being at war with the pope. Excommunications eventually end, there's no way to guarantee that the Pope will make peace with you. You can't get authority for a crusade as long as he's at war with you.

Here's what I did: I wiped the Pope out completely. I then pulled everyone out of Papal States (left people in Rome). Unfortunately, the Pope reappears in Rome, not the Papal States. So, he wound up declaring war on me all over again. I reloaded and thinking he'll appear in both provinces. Nope, the Byzantines took the Papal States, the Pope only took Rome. So I guess the answer is take him out completely, then abandon Rome and make an alliance with him as soon as he comes back.