I am not sure where you are coming from on this. The Legend of Zelda series is about a great evil that threatens the land in which a hero chosen by the gods (a child) is set forth on a quest to vanquish it. So every game in some way or another references gods.
It isn't the main point of the game, but it is referred to. The story behind zelda games is merely to put context to what you are doing. It isn't about gods directly.
I think you are going to find many games deal with gods or religion in some aspects. Without knowing what exactly is the issue I can't really say yes or no.