Hail fellow Elyrian!
I was thinking about religion in-game too when I chance upon your post. Actually I was going through whatever lore I can find and all I found was about religion, so I searched the threads. Not too sure why no one replied you though but here seems to be another discussion on religion that might interest you.
To answer your question, from my limited knowledge, it will seem that the only organised religion is the Vitori who are described to be "paladins and clerics." So if there is going to be a Pope like figure, it is most likely to come from the Vitori. Not too sure if this Pope is going to have the same powers to excommunicate people like CK II though. Nothing has been said but I highly doubt so.
Why do I think so? Because I do not think that the other religions look anything like organised religion and it simply does not make sense to have a mechanic in-game for only 1 religion. If I draw some parallels between what I read and what I see in real life, it goes something like this :
Qindred = Norse Paganism + Greek and Roman Pantheon?
Vitori = Abrahamic Religions + Zoroastrianism? (Note, Organised religion)
Faedin = Hinduism? (No, I really do not think Hinduism is organised)
Servants of the Two-fold Queen = Taoism? Jediism? (Nope, Taoism is not organised, trust me. Jediism? Fan Club.)
Atheist/Agnostics = Atheist/Agnostics.
P.S. Everything I have typed here is speculative and based on my on perception.
P.P.S. I know I missed out on Buddhism, Sikhism and Pantheism/Pandeism. Other religions? Well I don't know what I don't know.