This is not even the case of "agree to disagree". That's how facts are. If Bioware never did the extended cut then your argument stands true but the fact Bioware addressed the rather ambiguous ending means that any further analysis of the original ending is moot.
This. Seriously. BioWare can't (for PR reasons) come right out and openly repudiate the indoctrination theory (at least until it's necessary to do so), but the extended cut is completely incompatible with the indoctrination theory. Indoctrination lost, twice. They took it out before release, and refused to go back in that direction afterward. It's time to move on.