Possibly something to support the hallucination/indoctrination theory, though this is a long shot, is the parallel to Greek mythology. There are clear references to the realm of Hades, the Greek underworld, which is not a physical place, but a realm occupied by spirits of the dead. Cerberus, the guardian on the far side of the River Acheron (river of pain and sorrow, possibly represented by the path to the conduit), Charon (name of the Sol System mass relay) who was the ferryman across the river to Hades (Hades Cannon from the start of the Earth mission). There are 3 'judges' in the palace in Hades, possibly represented by Anderson, TIM, and the God Child. The judges could send a soul to 1 of 3 places: Asphodel for neutral, Tartarus for evil, and Elysium for good. "Lesser spirits" would also surround the hero, similar to the ghost-like figures in Shepard's visions. Also, leaving the realm of Hades was something only a great heroic figure could do.
It seems to me that after so many parallels, similarities, and references to Hades, it is atleast believable that the journey to Shepard's 'Hades' could be his ongoing indoctrination. He must cross the river, deal with Cerberus, face the judges, and then ascend out of it all (possibly the Destroy option, since he lives).
However, it is also possible that I am completely off-base and talking non-sense. There are many ways to interpret it all, and it is certainly a longshot, but I saw no harm in bringing it up.