It's not that the Indoctrination Theory is incorrect because it's bad. I mean, I think it's bad, but that's not why it's not the truth.
It's incorrect because all of the leaked statements from BioWare, including the infamous LOTS OF SPECULATION FROM EVERYONE behind-the-scenes bullshit, strongly suggests that they intended this ending and nothing more.
That's the problem here. There needs to be some sort of proof that the ending was intended this way, not simply that it Makes Sense. Of course it makes sense. Anything would make more sense than the Mystical Starchild and his Lucky Charms Rainbow Gun. Just because an alternate theory is sensible, though, doesn't demonstrate intent from the writer that it was, in fact, the intended result.