I say it goes too far because nothing in the movie supports it. It is quite reasonable for programs (were they sentient as in the movie) to look to users as creators, hence as gods. It doesn’t make sense to suggest the movie claims that WE are programs ourselves created by a being as flawed as we are. The movie just doesn’t go there.
Certainly movies can be a vehicle to try and push a political or theological agenda, but sometimes they are not intended in that way at all and they are just trying to entertain the masses. I don’t see any reason to view Tron: Legacy as pushing a theological agenda. Yes, there is a religious component to the culture it takes place in, but that is not the same thing. It is a setting and culture completely separate from our own. Likewise, Lord of the Rings wasn’t trying to indoctrinate us into elven theology.
As for Avatar, I didn’t see it so I can’t comment.
In other words, there is no such thing as allegory. In order for fiction to comment on matter of a religious nature, it must be explicit. That’s an odd view. But it’s yours to have.