Like the other commenters, I'm cynical and think they were okay with it for several factors:

1) conventionally attractive white lady
2) beefy all-American religious dude
3) the possibility of romance and conversion where the atheist learns the error of her ways


I quit watching the show after a few seasons because the writing and characterization were so weak and inconsistent, but it sounds like Bones ended up pregnant so... yeah. I bet that demographic was okay with it.