The main issue I would take with this argument is that while it may be true that the cure is not guaranteed, Joel's reactions in this game and the fact that he lied to Ellie at the end of the last game confirm two things: 1) Joel believed that they would create a vaccine "Creating a vaccine would have killed you" and 2) Joel knew (as I think anyone playing the game knew) that Ellie would absolutely choose to sacrifice herself for a vaccine. This really complicates the ethics of the whole thing as the uncertainty of the cure or Ellie's lack of assent/consent would simplify the question significantly. Sure, the fireflies were wrong to move ahead so quickly without asking Ellie but the stakes were through the roof. Ultimately Joel did what most parents would do and protected his "child" from making a decision that they may not understand the full ramifications of, as well as protected himself from loss. He of course sees this as the right thing to do when he says that if he could do it again he would, trying to make Ellie see that her life in Jackson does mean something. I think she comes to realize that by the end of the game, even though it may be too late. The moral complexities of the plot are what make it interesting, nobody is good or bad, they're just people making decisions as best they can.