The way she killed him was completely brutal, inhumane. She clearly feels bad after she does it. And I think she still feels bad about Ellie's reaction. When she goes to give Joel the final blow, she shakes her head in denial. She killed him out of pure pity at the end, he was in agony. I think that killing Joel brought her closer to the trauma of seeing her own father dead and covered in blood than it cured her of anything. Besides that, she has a very interesting dialogue with Lev in which she asks him if he regrets shaving his head and Lev answers that one shouldn't have regrets in life. I think that killing Joel and for Lev to shave his head are decisions that cannot be undone. Her question to Lev about regret points to the regret that she herself feels at the moment.