Why Joel made the right choice:
One thing that really made a huge difference for me was the fact that the doctors had a chance, a CHANCE at creating a VACCINE, not a cure, from Ellie's immunity. First of all there were no guarantees. This is the first time they've seen someone with an immunity so there's no guarantee a vaccine can be made. They just really believe it's possible. Second of all it's a vaccine not a cure. All you can do is prevent further infection. Infected can still tear you to pieces, a vaccine isn't gonna protect you from that.
Also, let's look farther than the creation of the vaccine. How do they distribute it? Will it be free? Does everyone get it or just the people the fireflies like? Creating a vaccine just brings up so many more problems. I can imagine a very clear scenario where the fireflies become exactly what they fought against all along. This totalitarian power that holds a shadow over the people. Instead of rations it's a vaccine. "But you only get the vaccine if you do what we say and think what we want you to think."
I also find it laughable that they think the vaccine will magically be distributed around the world once it's created. Marlene couldn't even get back to the hospital without getting her whole team killed, how does she think she's going to be able to drive all across the country distributing this fragile product?
Ellie's death would've been in vain and Joel made the right choice, selfish or not. There's no saving an already broken world. A potential vaccine isn't going to save you from bandits raping and murdering you. A vaccine isn't going to save you from a horde of clickers ripping your throat out. A vaccine isn't going to stop your legs from being blown off from a firefly terrorist bombing. The fireflies act as if a vaccine is a salvation for humanity when it's quite the opposite. It's a way for the fireflies to gain more power over the remnants of the government and the people that populate this destroyed world. It's a symbol of power for them, nothing else.
Joel will go down as one of my favorite characters of all time.
Thank you Naughty Dog.