We've got centuries of legal/moral/cultural norms built up around the idea that someone who can't clearly register their preferences in a life or death situation, that you treat it as though "help, I don't wanna die!" is what's happening. Again, this isn't about whether Joel's motives were clean or not, it's a question of "what is the right outcome".
I can't insist clearly enough - that Ellie's conversational assertions about "whatever it takes", "has to mean something", etc are substantively different from "hey, you're going to die, right now. Not maybe, not in a year. To accomplish what we want to accomplish, you have to die, today", and Ellie is a teenager. Grown adults are infamous for saying one thing and doing another when actually called upon, children doubly so. Marlene wants to take those abstract conversations as definitive consent; Joel doesn't care that she said it at all. Between the two, Joel's is closer to understanding real human behavior.
We can speculate all we want over how Ellie felt about it in theory OR how she felt about it after the fact is how she would have felt about it with a consent form in her face and people standing by ready to put her under from which she'd never wake up. But that's all it can ever be is speculation. Again, under circumstances chosen by the Fireflies, not by Joel. And in absence of that certainty, eleven words for which he should never apologize are these: "Making the vaccine would have killed you. So I stopped them."
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No, it is. We just rarely see it show up in the form of one life. Usually it's always a population. There's always some "greatest good for the greatest number" that can be maximized if only you are willing to smash your boot down on some group. It's the philosophy that has justified almost all the most depraved acts in human history - that this one life or these hundred or these several million don't matter against the abstract Greater Good.
TLOU was an object lesson that if you subscribe to that degenerate philosophy you better be better shots than those that don'tIf humanity can be saved by thee death of one you do it. No hesitation. And you do it with a smile on your face knowing the species survives. If you stop it from happening then EVERY single person from that moment on that dies from being infected or killed by an infected you have murdered because you allowed that to happen pure and simple.