@granderojo: I don't really see it in those terms. Ellie understands herself better than Joel understands himself. She is aware of the terrible things she has done, and what it is doing to her. She faces that reality. Joel on the other hand is a man who represses. He represses the significance of the loss of his daughter - he won't talk about it. He represses the significance of all the murders he has commited. And that is why he does the wrong thing in the end: He does it from a lack of understanding of his own motivations.
Ellie, on the other hand, knows she is probably going there to die. When near the hospital, Joel asks her why she is so quiet. It's because she realises what's coming. But she pushes on, because she knows it's what she has to do.
The Fireflies has lost their sense of humanity too though. In the eagerness to find a cure, they are able to murder an innocent. Marlene tries to justify it to herself, but again, her lack of understanding of herself, leads to the downfall of the fireflies. She lets Joel live. Because she won't fully realise what she has become, she wants to maintain the illusion of still having some humanity, and that makes her not walk completly down the road she has started on.
The "right" thing to do would have been to present Ellie with the choice with all the ramifications possible, and then let her make a concious decision to commit to the surgery or not. But neither side find themselves able to do this, and so it ends in tragedy.
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