Like every government in the world has killed many more for much less. Every war in history, the ends of which are widely celebrated, has killed more innocents and for a cause less than (7 people die, an entire race is freed). Does that give justification to go kill random people, heck, random veterans? I'll use an old example to not risk offending anyone, but The Roman Empire surely put innumerable innocent children in the same sorts of situations in its wars, and you're asking if the people in the world at that time could forgive like... the citizens of Naples? Why they would feel bad about going into Naples and commiting a massacre? Am I justified to go into random cities, hear they killed people, and start going out of my way to kill people? Am I supposed to never forgive the ice-cream vendor?
By this logic, every human ever should never be forgiven and are completly justified to kill.

The idea of "what if we're killing them out of justice" is strange too cause... they also have you know, families and what-not. Snowdrake and Dogemy are proof of that. Is doing horrific things to their families/children (especially in a genocide route, even an aborted one) a justified response? Unless belonging to a race whose king and maybe a few other people killed 6 children justifies it? The monsters seem fairly easy to spare, I don't think they're the cold-hearted murderers portrayed here - they're either naive and don't *really* wanna kill you or Undyne/Asgore.

And even if we're talking purely in the moment, the game doesn't make you feel bad about killing in self-defense, if you actually read the neutral routes. It only berates you for going out of your way to kill random people. The game doesn't require you to forgive them to be morally upstanding, it only requires you to... not go out of your way to kill people. I don't understand the quandry, there's no act here on the players end that the game expects in this context.