In my recent Genoese campaign, the pope wouldn't accept a ceasefire while I was excommed. When my king died, and the excomm was lifted, he accepted a ceasefire, then an alliance next turn. You need to wait for either your emporer or the pope to die so your excomm will be lifted so you can launch crusades. After the excomm is lifted, you should be able to make peace with the pope.