I don't believe they will say yes or no to the indoctrination theory but I wouldn't be surprise if we see a future DLC that actually adds it to the game. Bioware is known for listening to players and they know many are interested in this theory.
They could easily add in content like the Omega DLC, and build one where it actually has a side story where Shepard is fighting Indoctrination. This would be a cool way to add some interesting DLC content at the same time giving a wink to the fan base.
I would be down for an Indoctrination DLC that happens before the ending of the game. If they did they should add in Harbinger as the main enemy there so if the EC does not expand on him, then this DLC could resolve the feeling we didn't get to fight him, wither its with guns or best mentally- argument. I would love to see a inner fight between Shepard and Harbinger inside Shepard's mind before the ending of Me3 as part of an Indoctrination DLC.