The Fireflies haven't killed other people looking for a cure, they've done experiments on people that were infected. Fans like to bring up the tape recording from the hospital at the end of the first game as to why Ellie wouldn't have resulted in a cure, but that tape talks about other test subjects that were infected, not immune. Ellie is likely the first immune person anyone has come across since the outbreak. And by the time Joel wakes up next to Marlene they've run enough tests to know how it is that Ellie is immune - which isn't due to a strange brain chemistry, by the way, but because of a freak mutation in the fungal infection in her brain - and to know that if they remove it they can reverse engineer a vaccine.Thank you. That's one of the points I bring up whenever someone tries to argue Joel screwed Humanity, is that the game points out the Fireflies have already killed quite a few people looking for a cure/vaccine and it hasn't resulted in anything so far. There's little reason to believe killing Ellie was going to be the silver bullet they were looking for. And your point about the logistics of the situation further compounds the point.
There's also the unfortunate fact Ellie was unconscious and the fireflies apparently didn't bother to wake her up to ask her if she was okay with dying for potentially no reason.Does she even know that particular detail(I haven't play TLoU2 yet and not sure I will at this point)? Because the fireflies didn't give her a choice in the matter and while Joel did what he did for selfish reasons, he at least gave her the option to be able to make that choice in the future.
And Joel never gave her the option to make that choice for herself in the future, since a) he killed one of the few surgeons who could pull it off, and b) told i.e. lied to Ellie that her immunity meant nothing and wouldn't result in a cure. The reason he lies to her is because he knows she would've died for a cure, and would hate his guts if she found out what he did.