"Also, I shouldn't logically be in this situation! The Pope is at war with the one I'm at!
"You attacked the Sicilians! I'm excommunicating you!" "But you're fighting them as well!" "Uh...cancel alliance
...." "
Clearly this particular pope is either senile or a loon. It is your duty as a good Catholic king to send waves of assasins to kill him. Not only will it save the Catholic world from his mad ravings but it'll nullify his excommunication upon you.
Alternatively you could withdraw your forces from attacking the Sicilians, fight a purely defensive war or try to make peace, while at the same time have a bunch of priests preach good Catholicism in your lands.
Personally i'd recommend you kill him and do it quick before your provinces rebel. Happy hunting