If the Pope is praying to Jesus Christ he is praying to God. I know that is difficult for some Muslims to understand(seemingly), but one could think of it as a triangle, three sides of the same figure. In any event, from what I understand the Prophet Mohammed(PBUH) allowed Christians to pray at his Masjid after a meeting he had with a group of Christian leaders. So if the Prophet Mohammed(PBUH) didn't find a problem with allowing Christians to pray at a Mosque why should you second guess that decision now?
Finally someone brought this up, jee it really can be difficult getting people to think.