(spoilers ahead, obviously)
I see a lot of people saying “It doesn’t really matter that the science behind killing Ellie to create a vaccine makes no sense, you’ve just got to accept that that’s how science works in this world.” But it does matter! Because anyone presented with the choice Joel was presented with – keeping your daughter alive or creating a vaccine that could save millions – you would ask about said vaccine! You would demand to know every bit of the science and whether the makers of this potential vaccine really, REALLY thought they could save even a small portion of humanity by ripping upon your daughter’s brain. And in this case, the Fireflies clearly don’t know every bit of the science they’re willing to sacrifice a child for. Jumping straight to “let’s cut her brain out” is MAD.
Ellie deserved a choice! Heck, Joel outright says this in episode 6, nice bit of foreshadowing there-
And I think Ellie would absolutely have chosen to die for a shot at saving the world. But it would’ve been for nothing. In Joel’s mind I’m sure he thinks he sacrificed the whole world for Ellie and he’d do so again, but from an outside perspective, the world was beyond saving. The only real way out was to rebuild.