I really do believe that theory, there's a lot evidence backing it, and would explain some of the developers comments on Twitter since its release.
I'm hoping they'll expand on it with an update/DLC/whatever, instead of just going "Yep, you were indoctrinated, well done for working it out". I think it's a stroke of brilliance if the theory is true, and they give us the ending the series and the fans deserve after "indoctrinating" it's fanbase into believing the current ending is real.
It'd be great if it was a full on expansion, like the Awakening expansion they did for Dragon Age: Origins. Unlikely though.
BioWare are pulling a bigger troll than Konami did with MGS2/Raiden.