I'd disagree. Religion encompasses the practices and myths of their followers among other things, not just faith in a deity.
Thats true, as there are widely different views on deities. But the existance of those beings who are deified or demonized is virtually indisputable as Harke said. But thats why I think the ancient world is a better comparison to TES. Rarely did people argue the existance of the gods in those days, but many disputed over their natures or who should be worshipped.
And as for the TES religious factions, I'd have to agree with Harke, they're more similar to political factions with specific metaphysical/cultural views than modern religions. For example, most cultures regard Aedra as gods, while some would rather worship the Daedra(chimer/dunmer). While others viewed these beings as just powerful spiritual people and saw worship as primitive(like the dwemer). and then there is the psijic order's view which does seem to condone the worship of "good" spirits, but views them more like theosophy's "ascended masters" which are of the same spiritual essence as humans but have ascended to a higher level of existance.
I guess whether the factions can be concidered religious depends on how highly they esteem these "gods", not whether it involves a spirit. After all Dagoth Ur's sixth house was very fervent in its worship, yet its members were given "divine" power and he was basically just extremely powerful ancient sorcerer. And the mythic dawn exalted Mehrunes Dagon in a blind faith worse than most religious factions, while the player can just make deals with daedra like working with a typical quest giver.
So concidering all this, to go back to the original question i'd say the only comparison to a "pope" in TES would be any human religious leader concidered to have a higher level of divine authority than other people. But that can be compared to all sorts of real world religious leaders in history, from crazy cults to ancient egypt's pharohs.