Bones? Oh no! I love the show, and she is, in my opinion, the most intriguing atheist on TV.
Also, I love the occasional references to the backstory, in which she previously worked identifying corpses of massacre victims in Guatemala from the 1980's. And those were the Reagan years, and the guns and planes and helicopters and intel was all US supplied. So the writers are clearly politically progressive and socially conscious.
Could there be a power struggle between the writers and the directors/producers or whoever is in charge of the set and the camera and what shows up on our tv screens?