"the question is not whether games should address religion, but how." #wymhm

Issues of worldview, philosophy and ethics are being addressed whether developers intend to or not. Narratives, characters, settings and even complex sets of rules that govern one's existence within a game world are inherently loaded with meaning and interpretation of that meaning. Acknowledging this truth in a way that is both responsible and thoughtful does not mean creating a game that is needlessly preachy or offensive. In fact, if thoughtfulness is in fact a part of the process, preachiness and offensiveness is generally avoided and the game is even more interesting as a result.

While recent treatments of religion in video games aren't perfect by any means, they do demonstrate the possibility of treating the subject with care and nuance.