It could also be due to some external influence. Perhaps an enemy used some kind of mind - control or manipulation on Kushina. They made her think that Naruto was a threat, so she decided to disown him. In the Naruto universe, there are many powerful villains who could potentially do this kind of thing.
Well, it could be that they find out some 'dark secret' about Naruto. Maybe they think he has some sort of uncontrollable power within him that they fear. Or perhaps they are forced to disown him due to political pressure in the village. There could be a group of elders or powerful clans that demand it in order to protect their own interests or maintain the so - called 'balance' in the village.
One possible reason could be for Naruto's protection. Maybe she thought by banishing him from a certain place or situation, she could keep him away from a hidden danger that she knew about. For example, there might be a powerful enemy targeting Naruto specifically, and she believed that by making him leave, he would be harder to find.
One possible reason could be some sort of dark influence or curse that makes her lose her maternal instincts. Maybe a powerful enemy targets her and in order to protect Naruto from further danger related to her, she feels forced to abandon him. Another reason might be that she is made to believe false information about Naruto, such as that he will bring great disaster to the village in the future.
One possible reason could be a mission. In many Naruto - related stories, missions often take characters away from their families. Naruto might have received a highly important and dangerous mission that requires him to be away from Kushina for a long time.
Maybe she's been possessed. In some fanfictions, characters can be taken over by dark forces. So Kushina could be under the control of some evil entity and that's why she hurts Naruto.
Naruto might be extremely heartbroken. He has always looked up to his mother, and being disowned by her would be a huge blow. He could become withdrawn and start to question his own worth.
One possible reason could be that Kushina has a very strong and intimidating personality. In the Naruto universe, she was known to be a tough kunoichi. Naruto, who might be used to more gentle or reserved people around him, could be scared of her boldness.
One possible reason could be a misunderstanding. Maybe some false information was spread about Kushina being a threat to the village, and Naruto, in his role as Hokage or a powerful figure, felt he had no choice but to banish her to protect the village. Another reason might be related to some sort of dark influence or curse that made Naruto act out of character and banish her.
One reason could be that she lost so much time with Naruto due to her early death in the original story. So in the fanfiction, she's overcompensating for that lost time by being possessive.
In the 'naruto rejects kushina fanfiction', it could be due to a sense of self - discovery for Naruto. He may be on a journey to find his true identity and purpose, and he believes that Kushina somehow stands in the way of that. Maybe he has new friends or allies in the fanfiction that he values more and their ideals are contrary to Kushina's. So, to stay true to these new relationships and his own evolving self, he rejects Kushina.