The idea of restoring the Grid to the true religion of The Users vs. the atheism of the MCP sits particularly uncomfortably with this reading of the film. In so many films featuring Native Americans, it's intended to enforce the racist notion of white superiority and divine right.
Is this an accurate read of the film? Maybe, maybe not. I'd rather suggest that it's a interesting read, and worthy of consideration and thought on your own rewatch.
That all aside, I like Tron. I've enjoyed it throughout my life, and even enjoyed the sequel and the Uprising series. It's music, visual style, and the idea of getting "inside" the computer has had profound effect on my life.
That all said, it is a Disney film, and subject to all the expected Disneyisms that entails. That's not necessarily bad, as long as you're not expecting anything particularly deep, or sociologically insightful.