One thing is important to keep in mind: There is the Pope as in "the pope" and there is the Papacy faction of which the pope is the leader. Most of the time, but not always, they´re the same, but not when it comes to excommunication. For instance, alliance with the Papacy will not protect you from being excommunicated, but being at war with the Papacy doesnt always result in excommunication. It´s a bit schizophrenic, really.