Well, as with Gene Roddenberry's beliefs, I believe at least McCoy wasn't a Christian and regarded it--like how many religions today are regarded--as myths. It's been a while since I've seen Star Trek V so I don't know if any contradictions happened between the that movie and the line McCoy spatted out in Star Trek II:
"According to myth, the Earth was created in six days. Now watch out, here coomes Genesis! We'll do it for you in six minutes!"
(I don't know if Christianity's a myth or not, so please don't bug me about it, bug McCoy when you discuss Trek.)
So, while Kirk and McCoy may or may not believe a God or Gods/Goddesses are out there, I don't believe they're truely Christians. They might take lessons from the religion, but they treat them as stories, much like how we treat Star Trek as, even though Star Trek sometimes drops in a couple of lessons for humanity to learn.
Add to that, look at the negativity religion had, from statements that they're myths to having Gods slayed by Enterprise to invoking religion to justify terrorizing the NX-01 crew to how religion was viewed in a negative light in TNG episodes like "Who Watches the Watchers?", etc. Though religion in general may have not been viewed entirely in negative light, like how DS9 allowed the Wormhole Aliens to masquerade around as gods for Bajorans to indian tribe religions in TNG and Voyager being practiced.
So... *shrug* I wouldn't be so sure the characters are Christians.