I like that the last of us likes to remind us of how everyone is a gray character and that nobody is a saint. I don't call joel a villian, I don't call abby the villian.
people (abby fans mostly) may call me out on that if they want, but if anyone in that game (besides david) deserves to be called villian here is Abby's father. I feel bad for her, but I don't feel bad for him. I mean, Joel did wrong things but at least he was man enough to admit he did it all, while Doc over there was willing to kill a little girl without her consent and almost did it with no shame. And if abby didn't love her father and had no emotional conection to him, she would have seen how unfair he was.
I once made a post where I was talking about how everyone was being (not exactly a villain) but selfish and unfair in this scenario.
Marlene; because she wouldn't wait for Ellie to wake up to discuss it with her, to prepare her for what she was going to go through. Sure, she knew Ellie wanted to do anything to help cure humanity, but to die for it? Ellie didn't know that, and Marlene was wrong not to ask her first. Marlene was being overly selfish here because she was afraid to ask her. What if Ellie said no? She was choosing herself and others so she could live over a little girl who wouldn't even know she died to help.
Jerry; because as a doctor (no matter if it's in the post-apocalyptic world or the normal one, he should stick to the codex), he should never perform a surgery on a patient who doesn't consent to it (unless the patient is unconscious and it is to save his life, which is not this case). Jerry, as a doctor, should have known better, but he was unfair and selfish because he'd rather kill a girl who had no idea what's going to happen to her just to live his life in a world that'd be better because of her—while this kid would never have a chance to.
Joel; because he took the only thing that mattered to Ellie just because he was afraid of losing her. Sure, it was the right thing in his eyes (I would do the same), but he knew he was doing wrong by Ellie. Because when Marlene said "It's what she'd want... and you know it" there was this look on his face where you could decipher the fear he had for not respecting the girl's wishes. He knew this was going to have consequences. But he didn't care. She was safe in his arms, and that was what mattered to him. Selfish. Yet Joel was the only one who was being unfair, but at least he did it for love. For the love he had for the kid who he wanted to have a life that he knew she never had in Jackson, where he was headed with her.
Every one of these people would be selfish in Ellie's eyes, and some of them would even be so-called villains in this scenario. I don't think there's black and white; there's gray everywhere, but what I know is that this scene and everyone's decisions and actions are so complex that I fear none of us could ever cover it if we tried.