I think she suspects it, she could of been drugged for other reasons, I mean she has no idea what happened. But if she's smart she obviously knows something is up. I don't think Ellie was ever told that she had to sacrifice herself to save humanity, a lot of people assume that she was, but when was she told that? And just because she was feeling guilty and depressed towards the end, doesn't necessarily mean she was ready to die, I mean for most of the game she seems full of life and eager to learn about the old world. Then towards the end once spring starts, she suddenly seems very down and depressed and we are never really told why. I thought there was still a lot the game didn't tell us, especially about Ellie, we pretty much know where Joel is coming from but Ellie is very a interesting and complex character. In my opinion this game was left wide open for a sequel or two or three.