I have alot to say about the story, its just not very good in my personal opinion. The things these characters act out just dont make sense.
I am unsure how to create spoiler boxes so please dont read on after this point.
Joel killed her father, all of her friends and sabotaged the one chance they had to make a cure. He doomed everyone.
The reason she let Abby go at the end I believe is because of Lev. When she is drowning Abby, she sees a memory of Joel. The person who took care of her. Abby is like a Joel to Lev.