You know what I've found interesting? I killed the pope in battle after being excommunicated, then left Rome in the hands of a rebel army waiting for the Papacy to reappear. Sure enough they did a few years later.

They retook Rome from the rebels and all was peaceful for a bit, then they attacked me to take Tuscany. I fought the Pope off and he retreated. Now I'm at war with the Pope, but I'm not excommunicated.

Doesn't that seem weird? I would have thought that no matter what, if you're at war with the pope, you're getting Ex-comm'd.

Likewise, is it possible to be allied with the pope while excommuniated?