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.
Yeah i completely agree he had to die, however it was how it was implemented. There was no build up, barely any character development to lead into it, just a quick removal of the face of TLOU to make room for a forced story, thats how it felt.
I believe Lev was the reason too, but its not a realistic outcome for Ellie. She literally saw Joel get tortured to death by her, she saw Abby kill her friends, and Ellie cared little for any one to the lead up to finding Abby.. than all of a sudden gives her mercy? I dont know, it just felt unnatural.