It could be for shock value. Some writers might want to create a really out - there story to get people talking.
Well, one reason could be a desire to break all the rules and norms of the Naruto story. The writer might be tired of the typical fanfic plots and wants to create something that no one has really thought of before. Another possibility is that they are trying to make a statement about the fluidity of relationships in fiction, although this is a rather extreme way to do it. Also, it could be just a very strange and unique creative impulse, not really following any of the usual fanfic trends but instead creating something that is completely their own, regardless of how it might be received by the wider Naruto fan community.
Perhaps it's an attempt at a really extreme 'what - if' scenario. Like, what if the normal relationships in the Naruto universe were completely turned on their heads? It could also be that the writer wants to explore a very different side of the characters, taking them out of their normal roles and seeing how they'd react in such a strange situation. But this is a very unorthodox approach compared to more traditional fanfic ideas in the Naruto fandom.
Well, it could be for creative exploration. Maybe the writer wants to see how Naruto would turn out if he had a difficult family situation like being abused by his mother. This could then lead to a different path for his relationship with Hinata. It might also be a form of catharsis for the writer, expressing some darker emotions or ideas through this fictional and extreme scenario. Additionally, it could be an attempt to analyze the impact of a negative family environment on Naruto's development in the context of the Naruto - Hinata relationship.
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 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.
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.
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.
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.
Maybe some people just want to create shock value. They think by coming up with such a radical and out - of - place concept, they can get more attention.
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.
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.