actually the IT'ers have a point that Shep was indoctrinated before he was aboard the citadel. It's the only way the catalyst can communicate with organic life. All the dream scenes were the symptoms of indoctrination, as Sheps mind became accustomed to the wavelength, of sorts, of this channel. Very over powering, could even destroy Sheps sanity. The fact that Shep underwent trauma every time he encountered a form of reaper strong enough to emmit that signal,almost put Shep in the throws of indoctrination.
But something is different about Shepard, for some reason he can withstand it, barely, and able to communicate directly with the catalyst during their meeting. It always bugged me that these visions were always confused in Shepards mind, from the first beacon encounter to the time he was wisked up to the citadel. Who prepped Shepard for that. Getting strafed by a reaper molten metal beam isn't bad enough, to being removed from your body and end up where they take organics to get harvested,without getting reduced to random atoms is a strange thing.
Shep had to be in some sort of trancelike state on the ground, his intellect taken up that beam(kind of like when they harvest the DNA and memories) to talk it over and decide.In a sense, Shepard was indoctrinated, but only enough to be in state capable of surviving direct contact with the catalyst computer AI, who appears to be just memory of Shepards dream state. It's understandable that the IT folks feels that the whole thing is a sham and trap. The only hole there is that if the catalyst wished to just 'take over' Shep, why not use direct control? Cause it said that the IM wasn't able to control cause he was truely indoctrinated. Like Saren, unable to resist and keep their independent 'self' as it were.
just a theory taken from the game facts I experienced...