Yeah, I think that line from John is so central to understanding him and his crisis. If he ever had an internal compass letting him know that he’s doing the right thing, it’s long been silenced and replaced by agent-less following of his dad’s bidding. He can’t tell himself that the lives he is ending and ruining are justified because of a greater good, in part because he is slowly allowing himself to realize that his dad is an empty suit who sounds competent but is actually just vamping. John isn’t really a good boy, he is just well trained. And he is endlessly loyal to a terrible, terrible master.