Yep, making choices has consequences. But so has not making choices.
Indeed. Usually, when atrocities happen, one or several guys that nobody liked tend to get singled out as the sole culprits and punished as an example to all, while the people actually responsible for ordering them, and who continued to turn blind eyes to the whole thing until some journalist or whistleblower blew it up into international news, get away scot free.
There seems to be one exception to that rule, which is when an entire regime comes crashing down - in which case, some of the people ultimately responsible for atrocities will get caught and punished for it.
I suppose your best choice as a soldier, then, is to hope that the regime you serve falls quickly and gets replaced with one that will rehabilitate your legacy. Good luck with that - in the decades since WW2, it hasn't happened to the majority of Wehrmacht soldiers who were tried and executed for desertion, nor to the numerous Germans tried and executed for joining a resistance force.
So these are the consequences you face - cushy job with the miniscule chance to become a scapegoat months or years down the line, versus endless mistreatment by your employer with the likely prospect of becoming a fall guy for all of it when this all blows up anyway; alternatively, you could become a whistleblower and endure a decade in solitary confinement. And that's in a liberal democracy with at least a nominal commitment to human rights and due process; your prospects in an authoritarian regime are extremely likely to be much, much worse than that.
According to Sartre, we always have a choice, even while enslaved or tortured. I guess we can draw the conclusion from this that all the slaves and torture victims wanted to be there, or else they would have resisted. What do you think?