
To draw the line at 'you can't vaccinate against fungus' is foolishness.
"The Fireflies were wrong because you can't vaccinate against fungus so they were the bad guys and Joel was right to kill them."
Even if that were true, which it is not, why is the line drawn there?
Bearing in mind I'm primarily talking about the games here. I haven't watched the TV series, but from what I've gleaned from a bit of research it's basically the same thing, but with theories as to the proper explanation (mother infected while pregnant, I believe?). Onto the topic though;
Cordyceps can't infect real human beings. But we accept that because that's the rules of the setting.
Cordyceps does not turn insects into cannibals or otherwise make them eat other insects. But we accept that humans become cannibals in The Last Of Us because that's the rules of the setting.
Cordyceps doesn't actually control the brain in insects in real life. It hijacks the muscles and the poor things are along for the ride as it pilots their bodies and forces them to climb before self-destructing to rain down spores over a large area. But we accept that it grows in the brain in infected humans and they swarm in dark and wet places to die and spread spores because that's the rules of the setting.
Cordyceps doesn't mutate insects into more grotesque and disgusting forms that are stronger, faster, act different, blow their heads open and make them sense via echolocation or throw spore pockets that explode at a distance. But we accept that it does this to humans in-universe, because that's the rules of the setting.
Instead, the line is drawn at vaccinating against the Cordyceps using Ellie's infection. Because in real life, you cannot vaccinate against fungal infections.
But that argument is not valid. Because we don't know the rules of the setting in that regard.
Ellie is believed to be the first and most likely only person in the world who is immune to the Cordyceps - but she isn't immune to the Cordyceps, she is already infected with it. It just hasn't zombified her. We don't know whether it's a mutated strain of Cordyceps or if it's specific to her as a person down to the genetics (again, in the games, I'm not caught up on the TV series).
In order to even try to manufacture a vaccine out of Ellie's Cordyceps, they need to harvest it from her brain which would kill her in the process. What do they do next? Run tests, or slather the sample on a blade and stab someone with it then see what happens? Will it infect them and make them go zombie mode or will it render them immune to the actual zombifying strain of Cordyceps? It's not like all vaccines are vials and needles of a liquid that you inject into someone's arm. Did you know you can be exposed to cowpox and that builds up your immunity against smallpox, ergo VACCINATING you against smallpox? That would be the exact same thing as being exposed to Ellie's benign strain - if it worked and didn't zombify you. If it works, they are immune by virtue of already being infected by the benign strain, ergo VACCINATED against the malignant strain, am I not correct?
It's all 'if'. Not 'when'.
We don't know if it would work, thanks to Joel.
The Fireflies could have been right. The Fireflies could have been wrong. Joel could have been right. Joel could have been wrong. Yes, the Fireflies fucked up. They put Ellie on the table and under the knife without consent, goodbyes, or informing Joel about it beforehand. Yes, Joel fucked up. He killed a dozen soldiers and the three surgeons in that room to save a girl he treated as and thought of as his own daughter.
What matters is that Joel robbed the world of the possibility of a vaccine, whereas the Fireflies acted unethically, sent him outside without his gear which would likely result in his own death, put Ellie under to start the operation without consent or properly informing any party, and may or may not have killed Ellie in vain.
The vaccine may have worked. The vaccine may not have worked.
That is an intentionally unwritten rule of the setting.
To say that either side is wrong ruins the final conflict. It's meant to be ambiguous. You are meant to not know. And you cannot apply real life science to a fictional setting that already has its own rules just to say 'Fireflies bad Joel good'.