In response to the debate some pages back if Joel's choice poses a question of morality:
I think some are taking the word "vaccine" too literally. I believe it's just a short-hand for "a cure that works by preventing future infections in a healthy person". And that's exactly what the mutated cordyceps does for Ellie (also I remind you this is still a fictional infection even though it's inspired by a real one). It's quite possible that any number of things could go wrong with this plan because the Fireflies aren't exactly the strongest most well run organization. But what if in the world of the Last of Us they are the best option left? Seemingly the only choice if humanity is to have a shred of hope.
Joel saves Ellie for emotional reasons, although he doesn't believe in a cure either. Even so, I believe that there was a real possibility for a cure. And maybe the Fireflies really were the best bet to make that happen, as bad as they were. There wasn't much hope, but Joel traded that little spark of hope for a daughter. My point is, it is morally questionable if Joel did the right thing. People saying that "the cure would be almost impossible to mass-produce and distribute" are missing the point imo. For humans living in such a desperate situation, even a one-in-a-million chance to end it all could mean everything. And who knows, maybe those human's who have adapted to this living environment could be tough and resourceful enough to pull it off