*Spoiler-ish if you haven't finished the game.
What the Last of Us doesn't tell us is if Ellie is, in fact, the only immune person. Which I highly doubt that as it sounds statistically impossible.
From what I remember about a documentary virology there comes a tipping point where the virus has saturated its infection point in host organisms. If every host organism dies then the virus can no longer replicate. Now, obviously the fungus is fictional, but, if humans are a food source and a source of spreading how would it sustain itself if it rendered the population extinct? Nature, to me, operating on a system of checks and balances, produces a human genetically immune to the virus. If Ellie has done it I think it stands to reason others have the same immunity. Except Ellie is the only known person immune.
Now, from a sociological perspective, if I play out a scenario where Ellie had died and a cure was developed that'd give the Fireflies massive political power in the three headed power structure that includes them, the military, and the hunters. They would effectively decide who lives and dies. There is nothing indicating that the Fireflies would forgive and forget. They could extract all manner of concessions or simply let people they don't like die if they couldn't mass produce a cure. Worse yet, it could touch of a war for the cure itself.
So, concluding my thoughts, Joel was mostly operating on emotion and instinct. But on some level I really believe he didn't see the people like himself, the hunters, and Fireflies as worth enough of a damn to sacrifice Ellie for under any circumstance. It's selfish and morally apprehensible, but I can see reason to it from a macro perspective of what happens if a cure was developed. Again, doubt that was going through his head. But he clearly had time to consider things a bit when Marlene was begging. And he did not care.
I have nothing to back up my suspicion of others that share immunity to the fungus, but it's just my theory that some of the population would develop immunity. Leaving the remnants like Joel to die off. Probably for the best.
P.S. If any of my science is off base please don't take offense. I do not claim to be an expert.