Wait, I'm confused.
(SPOILER)People are debating whether Joel was telling the truth? I thought it was pretty obvious that he was lying. Ellie was the only chance for the Fireflies to find a vaccine, and Joel went all nuts because he finally saw Ellie as his daughter. He did the absolute wrong thing for selfish reasons, and then lied to Ellie. I can UNDERSTAND those selfish reasons, and feel sympathy for him, but he definitely did the wrong thing.

The epilogue is where I am a little more uncertain. We got another glimpse of Ellie's wound, and it seemed worse than it had been, suggesting that she wasn't completely immune, but could hold out longer than anyone else, and that was enough for a vaccine to be developed. That is why she asked Joel whether he was telling the truth. She wanted to know that the Firefly's are able to find a vaccine. Knowing this, she was ok with what she thinks happened. At least, that is my take on it.