I mean, the game did a really good job of leaving room for interpretation, so the answer can kind of be whatever you want. That being said, my understanding has always been that the implications that the main character was somehow responsible have more to do with survivor’s guilt and the psychological responses to abuse than they do with any direct involvement in the deaths. ie. the prophet/ess feels responsible, not because they did anything, but because they survived and because they have quite possibly been conditioned to feel responsible for the bad stuff that happens to them since that is pretty textbook in abuse dynamics.
I also get the impression that the Creator cult really didn’t need an excuse to hurt people. And killing arbitrarily keeps people from feeling secure, if it can happen for no reason, then it can happen to anyone. It might have been nothing more than a show of power to keep people afraid.