Ellie changed and remained the same at the same time.
Her change in both ways was because of the two major events, the one from the first game ending, which was always clear she knew she was being lied to, and the one from this game, which I won't talk about.
Ellie never agreed with what Joel did for her, and still she loved him more than her hate for his choice.
She was set to do what she wanted to do because of her hate, but she is not Joel, she can't do what Joel did, which is exactly why she hated what he did for her, even as she loved him even more than that.
On her journey Ellie realized what she needed to do to achieve her goal was simply not right, and every major char she kills makes she hate herself more and more for becoming like Joel, specially that one in the hospital which she has to get info from, she was cruel.
After meeting Abby for the second time and realising what Abby could do even after Ellie did what she did, that made she gave up on her goal for as long as she could, she didn't hate anymore, but her love for Joel was still haunting her for what she should do.
Then Ellie abandoned her happiness and the least she still had for her love for Joel, but in the end, she was stuck with what she had realized before, what she needed to do was simply not right.
Ellie tried her hardest to force herself to do it.
Ellie fought against herself and chose the hardest path, differently than Joel that chose the path that pleased only him, it was what she was always set to do, because Ellie was never like Joel.
The first time she shots someone on the first game she is immediatly not ok with it, and after she lets her hate consume herself against David, she loses her mind.
Ellie was never like Joel, she always wanted a reason to feel she was worth living like him, but she was never a cold person like Joel (which Joel turned into, after the outbreak).
Ellie was very faithful to herself to the very last, and she even lost her means to the only thing she still could be linked with Joel, which was shown in the last scene and very worked into during her trip, whenever she found one of those.
This game story is very well thought, even as its so cruel.