Let's forget for a moment about the additional scenes that Shepard actually made it to the Citadel. My focus is on Shepard's conversation with the Catalyst.
Before the EC, Shepard seemed to be in a daze, where he would seem very passive, very willing to just accept the Catalyst's explanations without question. This was very unlike Shepard, and gave merit to the IT, because Shepard seemingly blindly followed the Catalyst's doctrine, or "solutions". Hence it could be argued that Shepard was indoctrinated.
However, post-EC, Shepard has regained some of his fighting spirit. He now no longer just accepts the Catalyst at face-value. He wants further explanations as to the implementation of Control and Synthesis, and the consequenses of Destroy. Hell, he can even flat-out refuse the Catalyst now if he wants.
So my point is, is Shepard still being indoctrinated if he has the ability to question the Catalyst's "solutions"? I mean, Shepard even asks why the Catalyst is offering these new choices. To be indoctrinated, is to follow a set of beliefs (or a doctrine, if you will) without question. But Shepard is now questioning the Catalyst.
Shepard even says "Let's get this over with" before deciding. Personally, this further empasises the difficult choice Shepard has to make, but because of the sacrifice and repercussions of each. It's a choice he has to make (well, not have to, as he can always refuse

), even though he mkaes it clear he doesn't want to make that decision.
I thought the IT would have been a great way for Bioware to pull an epic twist. Now, after seeing the EC, I don't mind the endings as they are. Enough was shown for me personally to appreciate how hard that decision was for Shepard to make, and Bioware did a pretty good job in showing that Shepard's sacrifice was not in vain.
Would I have preferred the IT? Yes, most likely.
Is it now my head canon? No. Not for me.
I am interested to hear your thoughts on this