I think the point is that shooting shouldn't be a core gameplay element. It doesn't fit the rest of the game, in any way, and also has the sad demerit of not being very good in the first place.
Then you might as well Hotline Miami every shooter, because no shooter is going to be able to justify the amount of killing.
The story and the killing Drake does don't combat each other. The gameplay doesn't serve the narrative, but it doesn't oppose it either. Equally, any other core gameplay mechanic would fundamentally change the Uncharted series.
So either shooters shouldn't attempt to have a story, or no story based games should include shooting?