Eh... as intelligent as this was, and althought it brought up some interesting thoughts, I think you're digging to deep. And trust me, I LOVE to dig deep.
Yes, the Mario games never acknowledge that there is some god controlling them. But does it deny the idea of a god at all? No. In fact, it makes it seem more like my personal view on whatever created us. Some powerful being put one thing in motion and then sat back, got some popcorn, and watched the show.
As for your insight on GLaDOS and the guy from BioShock (still haven't played that, sadly, so I don't know exactly what you were talking about), that doesn't scream "you're being controlled by a god, and therefore god is bad" at all like you made it sound. The story wasn't about fighting against a "god" at all. It was about fighting for freedom from someone with power. That doesn't mean god. Of course, you were right about God of War
but that's a given.
So like I said, interesting, but felt a bit like you were grasping at straws to me.