Why does Amir inwardly struggle with Baba’s statement that there is only one sin? If you were Amir’s friend, what would you tell him?

Amir struggles with this because of the guilt he feels over his treatment of Hassan. If I were his friend, I'd tell him to seek forgiveness. If that wasn't possible, I'd tell him to make some kind of amends. In Amir's case, he's given this opportunity by Rahim Khan.