Well, we make that kind of judgement in the game all the time. We find camps of Raiders and know these guys are murdering and pillaging all over the Commonwealth so we kill them. While we can say gameplay has motivated us to do this, the fact is our Sole Survivor has taken it upon themselves to dish some vigilante justice. This despite the fact the terminals are full of humanizing moments for the various Raiders.
I know my Lone Wanderer walked into Paradise falls and killed every last slaver there by himself. Then he killed all the ones at the Lincoln Memorial. Also the ones serving Asher.
It's a very ubermensch-driven world in the Siegal and Schuster sense. The superhero needs to bring order to the Wasteland and must judge what is the right and what is the wrong because, otherwise, no one does and the world continues to descend further into chaos.
A heavy responsibility but one the Sole Survivor takes up every time they go wandering with the big iron on their hip (oops, wrong game).
Of course, you can choose to say X6-88 has bigger rights and the Institute's humans too. Which is how the game's Faction choices work.
Not choosing isn't a choice in the game.
But, ironically, if it was real life, that would be a choice itself that had the same level of consequences as inaction has its own price.