A twist to add to this Theory, may be grasping at straws, draw your own conclusions:
If Shepard is undergoing Indoctrination from everything after being hit by Harbingers beam, what if it's The Illusive Man's new indoctrination that is trying to take over his/her body, but after paragoning/renegading the hell out of him during said indoctrination (either ending in you shooting him or making him shoot himself), the Reaper's take over the indoctrination attempt. Since the Reapers "control" the illusive man this could be their plan to capture Shepard. This would explain the 3 choices a little differently/clearly (assuming you've unlocked all 3): The blue, control option, represents The Illusive Mans will, the green Synthesis option represents the Reapers will, and the red destroy option represents Shepards will trying to maintain itself.
Something to think about, probably reaching too far though...