The only evidence I have is that it's so obviously the way the story should be. That's good enough for me. It does not matter precisely what fallen demiurge corrupted the parable away from its original perfection.

ETA: Just to clarify, I mean that as far as I'm concerned, brains used as computing substrate is the real story, even if it never crossed the Wachowskis' minds. Just like some people say there was never a sequel (although personally I didn't have a problem with it).