It could also be a plot device to create drama in the fanfic. The author wants to explore how Naruto would react to being hunted by his own mother. This would lead to a lot of character development for Naruto. He would have to face this unexpected situation and find a way to clear his name while still respecting his mother. Also, it could lead to some interesting interactions with other characters who might try to protect him or help him figure out what's going on.
Another reason might be related to some external influence. Suppose an enemy of the village has the power to manipulate Kushina's mind or emotions. They could make her target Naruto by making her see him as a threat to her or the village. In the Naruto universe, there are many powerful jutsu that can control people's thoughts.
At first, Naruto would probably be extremely confused and hurt. He loves his mother and can't understand why she would do such a thing. He might try to find her immediately to talk it out.
In some really complex fanfic plots, there could be a prophecy or some sort of ancient power play involved. Suppose there is a prophecy that Naruto will bring great destruction in the future, and Kushina is made aware of it through some dark magic or secret organization. She might think that betraying Naruto now is the only way to save the village and the world, even though it goes against her motherly instincts. This would be a very convoluted and interesting take on the idea of her betrayal.
Maybe in this fanfic, the author wants to create a unique and dark plot. Kushina might be made to hate Naruto due to some kind of misunderstanding. For example, she could be misled to believe that Naruto has some connection to a great evil that she is against.
Maybe in this fanfic, there has been a misinformation spread about Naruto that makes Kushina believe he has done something unforgivable. For example, if false rumors say that Naruto is involved in something evil, Kushina might start to hate him without knowing the truth.
One possible reason could be for Naruto's safety. Maybe she has to go on a dangerous mission and believes Konoha is the safest place for him. Another reason might be that she is forced by some powerful enemies who threaten Naruto's life if she doesn't leave him in Konoha.
In some fanfics, there could be a misunderstanding. Suppose Kushina did something that Naruto misinterpreted as harmful to him or his friends. This misinterpretation could lead to his hatred. For example, if Kushina was involved in a mission that Naruto thought put the village at risk, but in reality, she had no choice.
Maybe it's because she sees Naruto's strength and how he has overcome so many difficulties despite her absence. She realizes that if she had been there, she could have made his journey easier. Also, she might regret not being able to watch Naruto grow up, miss his first steps, first words, and all those precious moments that a mother should be a part of.
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.
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.