I don't think he hates her. But out of all the members in Team 7- Naruto(suffered as an orphan and jinchiruki),Sasuke(suffered the trauma of his entire clan murdered by his brother), Kakashi(ashamed of his father's death,guilty for killing Rin,losing his best friend Obito and losing his sensei),Sai(made to kill his brother and become void of emotions) and Yamato(being a test subject). Every member has gone through worst things in life, except maybe Sakura. So now Kishi is giving her the worst part when everyone else is having a good life.