Why it had shot itself when such a code was placed in it again is abundantly clear. Not fear, but a certainty of the known.

"...he is guilty in the sense that he feels guilt, and the guilt is his. I understand that, too. I remember you saying that."

By Security's choice or not, it had still happened. It didn't erase the feelings that were there. Things occurred, and even if it wasn't someone's active fault, the blood still was there. Even if all sixty one of those people had woken up the next day like Helena did, it wouldn't alter the cause of death.