Im skeptical about whether or not this was the plan all along. It probably came up in meetings from time to time, and was even hinted at in points during the game. But the team wouldnt be handling the complaints about the ending in the way that they are if they had the ace in their sleeve the whole time.
That still doesnt mean that indoctrination isnt the route that Bioware will take. Right now, it probably looks like the easiest way to use fan feedback to shape the ending. But it would just be that: the easiest way out. It wouldnt address protesting fans real complaint about the lack of choice it would just force us down another path that would once again require separate endings. A good delaying tactic, but not a satisfying ending for Mass Effect by any stretch.
The root problem of the Mass Effect 3 ending was that it was very hard to come up with a satisfying way to incorporate hundreds of hours of player choice into a set of reasonable, engaging, and conclusive endings. In my mind, an attempt at the it was all a dream solution would prove that Bioware wasnt up to the task.