I don't think I agree
I've seen this attitude more and more of "Oh, why do games make me kill?" and I can never get behind it. Why? This is going to make me sound odd, but it's the gods honest truth. The folks over at Rage Select put it best: on some basic level, whether we like it or not, there is something intrinsically fun about killing in games. Maybe it's because we're used to it, but on some level there is some satisfaction in it. It's something that's easy to quantify as a measure of success, and easy to also understand the consequences of actions (not talking morally here, rather "What happens when I do X?") To me it's just something that I am willing to expect or accept if it is presented to me. You can have fun non-violent games, I'm not saying games are only fun when they're violent. I'm just saying that the intrinsic fun in killing in games is something of a shorthand for progression and success, sort of how a health-bar is a short hand for survival, even though in the context of the story it can seem ridiculous, even with in-cutscene deaths.
As for The Last of Us...I think this is because of the confusion as to what constitutes a regular protagonist. The folks over at Spill I think gave a good assessment in that "If you think of Joel as a traditional hero, you may feel off or angry during parts of the game. But if you view Joel not as a hero, not even as an anti-hero, but a borderline villain? That's where everything fits together." That's honestly how I look at The Last of Us. I understand Joel's situation, and I understand why he does the things he does. He's still a villain though, in so much as his intentions, while sound and understandable, are ultimately dark, and sometimes evil, in nature. I don't see the killings in The Last of Us as "Oh, in this world life is so cheap that you're lucky if you only get three near-death experiences a day." I see the killings as the means that Joel understands the world, and that for him it's not just what will you do to survive, but what will you do to live? The game has never been one about the survival of the human race for me, but rather an understanding of what one will pay in order to do more than just survive and actually live, to have a life, to feel alive.
At first I thought that the last Hospital section was your standard "Stealth game needs action section, RAWR!" but as I thought about it, I realized that maybe it's because it represents the very thing I was discussing, living over surviving. If all this ever was for Joel was a means to survive, he would've just left before starting shit, resigning himself to Ellie's fate. Let's say for arguments sake that he stays and wishes to save her, but is still concerned more on survival. His shoot-out sections would be considered reckless at best, suicidal at worst. I think, on some level, it sort of shows that for Joel he could simply sneak and survive, but it's no longer enough for him. If he does a shoot-out, he may be reckless, he may get hurt, he may even die, but at least he's living. I think, on some level, Joel enjoys the killing. I'm not saying he's a psychopath who gets a thrill from seeing people die, rather I think it helps him cope with the surviving/living conflict. I think when he's with people he cares for, whether it's Triss or Ellie, his purpose on living has to do with them, but when alone or his relationship with others starts to crumble, I feel that's when he becomes the most reckless and is more likely to kill, because for him, that's the only way he knows how to actually feel alive. It doesn't justify his actions, it doesn't make him sympathetic, and it doesn't serve to make him a hero. What it does do is show a villain that, on some level, disturbs us, and one we would be eager to call out on, if it weren't for the fact that, like Joel, things start to feel panicked, rushed, and tense when things get chaotic and we start having to kill. Like Joel, it can feel fun. Like Joel, we start to feel alive.