He made the right choice. Think about it. If Elle did have the cure and they pulled it out of her humanity would still be doomed, cause the real enemy all along was other humans. The zombies are pretty much under control it's the humans that know how to shoot a gun, the war starters, the cannibals, the invaders, and the kidnappers that are the real bad guys.
Joel realized that humanity can't be saved because society have already collapse and no cure is bringing it back, so why sacrifice Elle?
Not to mention the fire flies would have likely used the cure to subjecgate the rest of humanity.