Guys, this is a forum about mount and blade, a video game, not about your beliefs. Take it to /r/athiesm why don't you?
I wouldn't mind anything that adds a new dynamic to the game. Religion being a big part of medieval culture would not be out of place, and it's pretty easy to say who's going to be who if we use real religions.
Essentially if it worked like Medieval 2 Total War where you had to spread you religion and such, than I don't see a problem.
Swadians - Catholic
Rhodoks - Catholic
Vaegirs - Orthodox
Sarranids - Islamic
Nords - Pagan
Khergits - No official religion
Khergit lands would start with a mixture of pagans, orthodox christians, and muslims.
If we could somehow add a new Japanese faction and some new landmass they'd be Shinto-Buddhists.
Since we have treeless trooptree's or however you put it, this would work out great. Catholic faction would get order troops (Hospitaller, Templar) Nords would get troops dedicated to the god of war, Sarranids would get Hashashin.
Now if only the game had a Jerusalem equivalent (the holy land) or some sort of papal faction that determined crusades/jihads.