Bioware won't touch the topic of Indoctrination Theory...but I would bet money that the EC will not say no fully to it but will not use the Indoctrination Theory in it. They will just add in new details on the existing ending.
But a certain number of the fanbase that's interested in the Indoctrination Theory.
I can see Bioware releasing an Indoctrination DLC that explores the concept of Indoctrination but this content would be before the ME3 ending, I mean before the return to Earth. It would be like any DLC, a section of it's own and would not change the ending.
@mimartin- Don't worry Bioware will not be jumping on the Indoctrination Theory train lol
They have defended their vision for the ending, they won't change it. The ending will stay as it is in the Vanilla game. =)