From what Weekes said about Hudson's writing process, Indoc theory is not correct. The ending we saw is what was literally intended. And I strongly doubt they will be retconning indoctrination theory in. in fact i doubt they will retcon anything... my guess is that they will just tack more content on to provide more closure. even if you don't have a problem with the events of the ending, they left a whole lot wide open. who knows what the hell happened to practically everyone but the handful that made appearances in the cinematics.
I also believe they intend to have some DLC dealing with the garden world and the crashed Normandy, I think they'll weave the outcome of that into some kind of fuller ending.
Everybody good, plenty of slaves for my robot colony?