Again, I haven't played the first game in a few years now (I plan to replay it soon, before I try the second one), so maybe my memory is rusty. But I remember the narrative thrust of the game's ending was basically that Joel makes a selfish decision to save one person rather than sacrifice her to possibly save millions. Then he lies to her about it. Whether you agree with what Joel did or not, it was clear that the narrative was, while not outright condemning his actions, at least trying to present them as morally ambiguous.

I don't remember Joel ever expressing doubt that the Fireflies could make a vaccine, nor did he make any attempt to talk them out of it. So this idea that he did what he did because he had a better understanding of science than the Fireflies did doesn't fit. It felt like Joel did believe they could do it, but had a last minute change of heart and decided Ellie meant more to him than saving the world did.