Story villian as a god?

I've come up with many ideas for fantasy stories, but before I even considered writing, I came up with a trilogy story dealing with a normal boy ending up in a fantasy place and needing to find a way to stop the villian to save everyone. The only thing is, the villian is a god and the end result wouldn't necessarily have the god being destroyed. The people who lived in the land were divided on their beliefs and trust in the god morally. Some feeling he/she is doing things the wrong way, others, honoring him/her. There's a villianous quality to the god and I do now how the boy will deal with him/her in the end. The only thing that kind of paused me was the fact that the villian was a god. It feels a little controversy, but that is how the story goes. I do know there are other stories that do invoke such religious ideas in their tales.