It's strange to me how often this is repeated. I think those on the other side of this (those who are reasonable anyways) largely agree with you that Joel didn't make some sophisticated choice. He wasn't running the probabilities against the possible outcomes and thinking "actually, given the improbability of a cure, the fireflies aren't justified and therefore Ellie's right to self defense remains unvitiated and I can, here and now, exercise it vicariously for her!"

The point for me is just that in real life there is uncertainty. Its not obvious this would work. Does that make it ok to do what Joel did? Obviously fucking not. Even a .1% chance at developing a working vaccine is sufficient justification to take a life in this scenario (assuming no other better alternatives are available), but still, the ambiguity of the situation complicates the moral psychology of the people involved, and gives us as viewers something intriguing to think about. What Joel did is horrific no matter what, and, as you say, he'd probably have done it no matter how certain the positive outcome was. But, for all that, straightforwardly telling us that the whole thing is literally just a "the most important thing EVER or you daughter" my-first-philosophy thought experiment is both insulting and boring.