You could take ludonarrative dissonance stance against the Uncharted series and I wouldn't argue against you. On paper, Drake is a mass murderer. However, I'm sure Indiana Jones could be convicted of 1st, 2nd, and 3rd degree crimes of the same kin.
Regardless, I would say that The Last of Us is the polar opposite of ludonarrative dissonance. Violence is a character in that story. The loss of innocence in Ellie throughout the first game is an integral through-line and, in my opinion, why that story is so impacting. Joel has 20 years of nothing but "kill or be killed" written into his DNA, and when presented with reigniting the father-daughter relationship he lost out on, he has to balance the person he is and the stark realities around him, while wanting to build on that same familial dream that was abruptly and prematurely taken away from him. The Last of Us is a masterpiece, again--in my opinion, due to this tightrope walk and intricate kinship between these two characters, and the fact that Joel makes the selfish and arguably wrong decision in the end and decides to lie about it to the one he loves, I'm even more curious how this plays out in the sequel.