It is also ironic as pomegranates are symbolic in muslim culture as a cure for hatred and envy, the feelings Amir has for both himself and Hassan respectively.
In the book The Kite Runner Hassan and Amir hada special Pomegranate tree that thy would go to together and read. Amir would read the stories he wrote or others to Hassan. The boys spent some of their closest times there.
After Hassan is raped and Amir had done nothing to help him, Amir struggles inside o cope with his own failure to help Hassan. The memory of Hassan's rape and his own failure to help eats away at Amir .
Amir projects his self-loathing onto Hassan. He is sitting under the pomegranate tree and he asks Hassan if he hit him what would he do. Hassan said nothing. Amir hits him with a pomegranate and tries to get Hassan to get angry at him so he can fight him. Hassan has only love for Amir and does not understand his behavior.
amir throws pomagrantes at hassan in a way of punishing himself, he does it because he is mad at himself. its not hassans fault.
amir had to pee and hassan loved him