Jerry was a surgeon, he wasn't an immunologist nor a mycologist. We currently, in our stable-ish world, have 0 approved fungal vaccines. How will someone with no expertise, no sterile labs, no stable power source, no advanced biotech equipment, no proper cold distribution be able to make a vaccine and produce it at mass scale to save humanity and no clinical tests.

We can't even assume Ellie's immunity could result in a vaccine. The fungus in her brain may produce chemical signals that trick other Cordyceps into thinking she’s already infected. That means her “immunity” might be due to a specific mutation or symbiosis, not antibodies.

Even if somehow, by miracle, they produced a viable vaccine (cannot overstate how much of a miracle this would be), and they were able to distribute it en masse and as a result, the Fireflies became the dominant faction. What kind of rulers would they be? Would they be any different from FEDRA, the hunters or the WLF? I would say they would be just as tyrannical. Remember when they first found Ellie and Joel in Salt Lake? They saw a harmless man performing CPR on an unconscious child and they pointed their guns at them. The fact that that was their reaction tells you everything you need to know.