The institutions of the state act a lot more like a machine, because the people in it are punished if they don't follow orders. While "just following orders" has been established in the past as no excuse, I think we've also shown through Stanford and Milgram experiments that human psychology does act that way. Thus, I don't think it's trivial to convert it into a moral agent problem. It's more of a systemic issue.

Ensuring there are consequences for people who act immorally may help address the systemic issues, of course.