One possible reason could be that Konoha has a history of dark secrets. Maybe Naruto and Kushina discovered some unethical practices within the village that made them lose faith in it. For example, the way the village treated the Uchiha clan was quite unjust. Kushina might have known about some of these underhanded dealings and passed on her concerns to Naruto.
Another aspect could be related to the way Konoha treated Jinchuriki. Naruto was ostracized for being the host of the Nine - Tails. Kushina, as a former Jinchuriki herself, would understand the pain. If the village continued to have a negative attitude towards Jinchuriki even after Naruto's many contributions, it could lead to their hatred. Konoha's failure to fully accept and support Jinchuriki could be a major factor in their dislike for the village.
One possible reason could be that Naruto might feel overshadowed by the Konoha 12. They all have their own unique skills and family backgrounds. For example, Sasuke is always seen as a prodigy. Naruto, who grew up lonely, could feel a sense of envy or resentment towards them which might be explored in the fanfiction. Also, the Konoha 12 might have some unspoken rules or a clique - like environment that Naruto doesn't fit into, making him develop negative feelings in the context of the fanfiction.
The first consequence could be a breakdown in the village's unity. Naruto is seen as a hero in Konoha, and if he turns against it, many of his supporters might be confused or even follow his lead. This could lead to internal strife within the village.
The relationship between Konoha and the Uzumaki clan might be further strained. With Kushina leaving, Konoha would lose an important link to the Uzumaki. And other Uzumaki members might see this as a sign that Konoha is not a safe place for them.
One possible reason could be for his safety. Konoha is a well - protected village with many skilled ninja. She might believe that leaving him there would ensure he has the best chance at survival and growth as a ninja. Also, she may have some mission or obligation that forces her to leave him behind, perhaps something related to the greater good of the village or the ninja world in general.
Well, in some fanfictions, the idea of Naruto hating Kushina might be a very dark and twisted take. Maybe the author wants to explore extreme emotional scenarios. As for Naruto loving in this context, it could be about different kinds of love - like platonic love for his friends or a romantic love for a character. Fanfiction often takes liberties with the original story's relationships.
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.
Well, if Naruto and Kushina left Konoha in fanfiction, it would change a great deal. Naruto would not have the same relationships with his friends like Sasuke and Sakura. He might develop different fighting styles as he wouldn't be trained by the same people in Konoha. Kushina, being a strong kunoichi, could train Naruto in her own unique ways. And their departure could also cause a stir in Konoha, with some people trying to find them and others realizing the mistakes they made in how they treated Naruto and his family in the past.
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.
One scenario could be that Naruto discovers some hidden secrets about Minato and Kushina that he interprets as them being selfish. For instance, he might find out that they had a choice to be with him but chose something else instead, which makes him angry and full of hatred towards them.
Maybe in the fanfic, Naruto has faced too many political intrigues within Konoha. He has always been loyal to the village, but if he constantly encounters backstabbing or unfair treatment from some of the village's leadership or clans, it could lead to his weariness.