I don't think he's wrong about how you're not supposed to take the number of people Drake kills as a literal body count. Except that a decent number of people DID notice a disconnect between Drake's character and the number of dudes he kills, even with the understanding that it's an action video game with guns and, yeah, you're expected to kill people. I couldn't really tell you why it's Uncharted of all games that suffers from this. Is it somehow justified better in other games? Are there elements of Drake's personality that make his body count especially egregious? Is it just a matter of the technology being good enough that we think of Drake as "more human" than a Bayonetta or a B.J. Blazkowicz? But I think these questions are worth asking when it comes to making the next Uncharted. Maybe Druckmann and co. have asked themselves these questions and have decided their comfort zone is different, which is fine, but I do think it's worth considering your audience's comfort zone as well.
That said, I'm guessing most people don't think very hard about Drake's mass murder, so in that sense Druckmann's making the right call.