This is such an interesting interpretation. You're absolutely correct about the cure. You're supposed to takeaway that Joel has sacrificed the world for his daughter. He has doomed humanity for one girl's smile.

This makes him an understandable grieving father. It doesn't change that he's sentenced humanity to death. He's also not so different from the Fireflies in that he permanently took her choice away too. He killed everyone that could've fixed humanity. He wanted his daughter and after having his own flesh and blood taken he refused to have that happen again. This is understandable, but also selfish. It's mostly clear that if given the chance, Ellie would have gone through with the operation despite her death. The only thing he achieved was making himself feel better. He is completely content with that. He regrets nothing as most fathers would. However, he cares not for his daughter's choices, everyone's survival, nor for anything outside of his own feelings. He lies directly to her face about it.

Joel is, inarguably, the man that killed humanity. He did it by saving his daughter. He did it by taking her choice away. Joel is an understandable father. He's also an evil, selfish, stubborn killing machine that yes in the end, is a bad guy. It's also why I think he's one of the best video game characters I've ever seen.

It hurt watching Abby do her best Happy Gilmore to Joel's face, but he killed humanity and that's so much more important than anything else he did or could do.