Yeah, but they do kind of make it contradictory: Shepard tells Hackett (damn you autodialogue) that the cost of Sanctuary was too high and that there was no moral justification for it. Then he tells Joker that Cerberus succeeded at their goal, and could justify it by telling himself that the people were going to die anyway. Not ideal by any means.
I hear you. I never bought the whole "disabled the dreadnought in good faith" thing either (gee, thanks, they're all still shooting at us. Are we supposed to pretend it'll
stay disabled?), and autodialogue damns Thessia too.
Tevos: "I never thought this day would come."
Shepard "
None of us did. I'm... sorry. You were warned
three years ago, Councilor. Nobody gets to hide anymore."