What happens if you don't get him to shoot himself? On my playthrough I used the charm options every time and he "did a Saren". Does Shepard take him down if you don't manage to talk him out of the indoctrination?
As far as I can tell, the crew members that step off the Normandy are Joker, your LI, and your final squadmates (or just one of them) from the rush to the Citadel beam. The conscious decision to make at least one of those characters somebody who WAS WITH YOU when Harbinger took everyone down just furthers the infuriating nature of the ending.
He forces you to shoot Anderson(somehow), then you get a renegade interrupt to kill him