If you must know, I think that it's just a reflection of contemporary distrust and hatred for organized religion that is being added in to make the titles more relateable.
Let me give you another view on that.
When it comes to games involving fear the idea of religion can be for four other reasons.
1)To unnerve you as someone who might take comfort in religious beliefs. Something that calms you is now in front of you, and trying to kill you.
2)To create an atmosphere of confidence agaisnt you. Your enemies are not afraid of you. Life and death are the same to them, and they will pursue you relentlessly. It adds a desperate feel.
3)They are presented as a cult* more so to scare older gamers with kids. Cult* worship is something that scares people with children. It can add a level of fear parents might feel that we don't.
4) Its easy.(explained lower)
*Cult in this case is referring to any non-major religion that's tenants are unknown. Thus the fear for parents.
While there is more though these are the primary reasons i see them added to fear based games.
The scientist in Dead Space that's helping the necromorphs is creepy as fuck for no other reason then in a midst all this chaos he is calmly walking the halls assisting them in there goals, and not dying.