To be honest, I do see this dichotomy, and it was something I struggled with while writing the story. Ideally, I think it should be up to the player to decide the feelings of the main hero. Unfortunately, this would have huge implications in terms of story branching (and therefore production complexity), so it's not entirely feasible for a one-man development "team". So my solution is a certain amount of ambiguity in the protagonist's feelings about the situation, which will manifest in later chapters.
As for "killing and getting killed", let's be realistic, a normal average person doesn't go around killing people. At this point in the story, I don't see the main hero being cornered enough to resort to any drastic measures.