I think he is saying that the movie dispenses with the notion of an all-powerful God, not the faith traditions it draws on.
The first movie did the same thing, Tron thinks everything Flynn is doing is according to a plan, and Flynn tells him, nope, he’s just making it up as he goes along. It has always been in the Troniverse that programs look to users as gods, but it really goes too far to suggest the movie writers are trying to say something about God and religion in the real world.
How does that go too far? Science fiction is one of the most effective mediums for social commentary. Did you feel the same way about Avatar? Did that film have nothing to say about the real world?