Other M was given a lot of shit but that was for things other than what you are arguing about. Older Metroids don't really justify going around extincting a whole planet's populace of different kinds of animals but it's a game and the animals (mostly) look mean/disgusting so no one gives a shit when you smatter their brains onto the walls of caves & buildings. The henchmen in Uncharted are no more meaningful. They are bad guys who are out to shoot & kill you on sight.
Actually Metroid games usually don't need to give justifications about all the killing.
You're a bounty hunter on a mission to do something using any means necessary.
In Metroid 1, you're infiltrating a base and have to destroy an army. Yeah she's going to kill everything on sight.
Metroid 2 is literally "go kill them all" the game.
There's no dissonance here : you're a baddass super hero in armor killing everything on sight, the gameplay and the story help each other.
Only in Other M where they try to shoehorn some kind of narrative like the bounty hunter that go on extermination missions alone and blow up planets is somehow some fragile thing.