Uncharted doesn't do that, though? The body count is ridiculous and it makes Drake come off as a complete sociopath if you think about it too hard but that's... pretty much it. You're not required to ignore anything; there isn't some great disconnect here.
You are literally proving my point here.
You could say the same about most action games, really, but I only ever see it blown out of proportion for Uncharted for some reason.
No, actually you can't.
In Halo, the protagonist is a soldier meant to kill.
As is in COD, Battlefield and all other military themed games from Wolfenstein to Destiny.
In Max Payne, TLOU, The Darkness etc. you kill people because they are revenge stories where the protagonist WANTS to kill people as the core of their motivations.
The reason you see this criticism so often for uncharted is... because uncharted has this issue more than most games. Literally what we're talking about.
TLoU is a "serious drama", though. Uncharted is Indiana Jones-style pulpy action-adventure schlock. Apples to oranges. The action in Indiana Jones doesn't exactly have big thematic significance either. And like I said, Indy only ever fights one or two dudes at a time but I'm not sure going that route would improve an action game like Unchated so I ask you again: what are you suggesting as an alternative? Should the narrative be strictly about how much of a psycho Nate is? Should shooters not be allowed to have a light-hearted story?
I already told you, write a story that fits the gameplay.
Borderlands also has a lighthearted story.
Even the Wolfenstein or Doom Eternal have lighthearted bits.
And all these games still narratively acknowledge that the gameplayloop is about killing people.