No one was in the right. That's why I was initially a little disapointed with the outset of the game, with joel's emotional heroic act of mass murder. It felt like the typical american movie (and to some extent people, but that's another topic) manicheit logic of Absolute Good vs. Absolute Bad. And saving lifes is always in the Good. Well, what life is more worth saving, millions of strangers, or that one cute girl you have grown into?
But my point isn't even that one. I actually question Joels reasons. He didn't save Ellie thinking on her. He was thinking on HIM. The way he found to cope with the death of his daughter was by toughnig up and frozing his heart down to a ice rock. Throughout the game, Ellie progressively woke his emotions up again, by her lighthearted spirit, jokes, and insistance on touching into personal topics that Joel had avoided for years. Now that he was re-humanized, he sort of grew overly atached to Ellie almost in a parasitive way.
I say this because the way I took it, Ellie suspected her fate could be death, and was willing to do it if necessary. I've seen people say she was quiet on the last city because of the winter events. I think it was only that day, joel said "why are you so quiet today" when certanily there has been a lot of time between her David situation and them getting to that last city. Ellie says a bunch of vague stuff that points to her knowing that might be her last day. She even gives Joel's family picture back to him as if that was her last oportunity. Joel just doesn't realize it because he is too busy enjoying his new pet-daughter, and is being rather insensitive with his talk about future plans or how he wished Ellie would have liked his daughter. Her end-game speech is all about how she felt like she didn't deserve to be alive, and how many people died just so she could get to the fireflies, so she'd better be certain joel wasn't lying.
Yes the fireflights way of handling the situation was also shady and wrong. They were desperate. And yes they could end up sacrificing Ellie and not get the cure anyway. And yes Ellie didn't spell it out that she would acept going through the procedings ( which was a mistake of the FF cause if they had her sign a paper, I think she would've). But that didn't happen. Joel had to imperfect choices. Let Ellie die despite the incorrect way the FF were hadling the whole thing, and despite the fact that sucess is not guaranteed. Or Kill a bunch of people and take Ellie out without consulting her.
I think the prospect of fiding a cure, even if faint, is worth sacrificing a life on a world were life has grown this fragile. Death is really not that uncommon anymore. But most importantly, the sacrifice was worth it because Ellie though so. Joel was as desperate as the FF on his rescue. Nobody actually heard what the actual immune girl wanted to do, she was treated as 'cargo' by both. And I think that's why the ending is awsome. It's crude, sad, but real. And hell of strong.