It might be due to a cultural or traditional misunderstanding. In some fan - created cultures within the fanfiction, there could be a certain act that Sakura does which is considered a great insult in Naruto's eyes. Without fully understanding the implications, Naruto punches her in response. For instance, if there's a custom about respecting the Hokage's symbol and Sakura accidentally desecrates it in Naruto's presence while he's in a very patriotic mood.
A reason could be that Sakura says something really hurtful to Naruto about his dreams or his abilities. Naruto, who has always been sensitive about those things deep down, might lose his temper and punch her.
Perhaps there was some sort of dark influence at play. In the world of Naruto, there are often dark forces and genjutsu (illusion techniques). It's possible that Naruto was under the influence of a genjutsu that made him see Sakura as a threat, so he punched her in self - defense without realizing it was an illusion.
She might leave to find herself. In Konoha, she has always been defined by her relationships with Naruto and Sasuke. Leaving gives her the chance to figure out who she is on her own terms, away from the expectations of her friends and the village.
He might be mind - controlled. Some dark magic or an evil character could take over Naruto's mind and force him to act against the ponies in the MLP world.
One possible reason could be that she might have underestimated Naruto in the past. She often belittled his abilities and dreams, but as she grew and realized his true strength and determination, she felt the need to apologize for her previous behavior.
One reason could be that Naruto has always been more attracted to those who understand his outcast past better. Sakura doesn't really have that kind of connection with him as she comes from a more normal background. So there's a lack of that fundamental understanding between them which hinders any romantic feelings.
One reason could be jealousy. Suppose Naruto had achieved something that Sakura deeply desired for herself or for someone she loved, and in a fit of envy, she took drastic action. But this would be a very out - of - character move for the Sakura we know from the original series.
Maybe Naruto is sick of Sakura in fanfiction because her character is often portrayed as too pushy or one - dimensional. In some fanfictions, Sakura might be overly obsessed with Sasuke and Naruto just gets tired of her constantly going on about it.
In some fanfictions, it could be due to unrequited love. If Naruto has deep feelings for Sakura but she continuously rejects him in a cruel or thoughtless way, Naruto might feel angry enough to seek revenge. For example, she could publicly humiliate him for his feelings, which would hurt Naruto deeply and lead to thoughts of revenge. Another reason could be a misunderstanding. Suppose Sakura is misjudged by Naruto as having done something terrible when in fact she was innocent. But Naruto, in his ignorance, decides to take revenge. This can create a lot of drama and conflict in the fanfiction.
One reason could be jealousy. If in the fanfic, Sakura gets closer to someone else Naruto cares about, like Sasuke in a different way than he expected, it might make him hate her. For example, if Sakura teams up with Sasuke against Naruto's wishes in the fan - created plot.
One reason could be miscommunication. Maybe Sakura said something that Naruto misinterpreted as an insult to his dreams or abilities. For example, if she made a comment about his progress as a ninja in a way that came off as dismissive.