To make it clear, this is not a debate about atheism vs. religion, or even one playstyle vs. another. Real world history is also irrelevant.
The point is, religion giving bonuses and special gameplay aspects is fine, as long as it has requirements equivalent to other professions or gameplay paths. It should not be a different type of path that is basically required. Religion should be one of that character's primary focuses, and take up time and energy like anything else would.
If religion offers bonuses with very little required of the player, it basically makes it a requirement of all players unless they want to be at a disadvantage. This is not good, because maybe I don't want to have religion as part of my character.