People weren't in immediate danger of extinction. You still had the military, large bands of hunters, civilians who lived in the military controlled zones, and independent survivors like the people who lived at Tommy's Dam. It seemed clear that there were still hundreds of thousands of people in the US, if not millions. People were in danger of dying or becoming infected, but there were still ways to survive. Tommy's Dam was able to keep out infected and fight off bandits, and while some inevitably would die, most would survive and be able to procreate.
PS- There's no way of knowing if a vaccine would have worked in the first place and even if it did, there was basically no way that The Fireflies could have produced it on a mass scale or distributed it to everyone. The military and the hunters and almost everybody else were paranoid and often shot on sight, especially the hunters. The only sure thing that would have happened if Ellie's surgery had gone through was that Ellie would have died. Joel's decision to save her was completely understandable.
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