It could also be due to a misunderstanding. Minato might have been misled by false information about Naruto. For example, some false rumors about Naruto having uncontrollable power or being associated with some dark forces could have made Minato believe that banishing Naruto was the best option for the safety of everyone.
One possible reason could be for Naruto's protection. Maybe Minato knew of some great danger that was coming for Naruto and he thought that banishing him would keep him out of harm's way. Another reason might be related to some prophecy or hidden power within Naruto that Minato feared could be misused if Naruto stayed in the village.
Perhaps Minato was forced to banish Naruto. There could be political pressure within the village. Some powerful and conservative forces in the village might have seen Naruto as a threat due to his status as a jinchuriki. Minato, being in a difficult position, had to make the hard choice of banishing his own son to maintain the peace and stability of the village.
One possible reason could be fear. If Naruto was 'godlike' in this fanfiction, his power might be uncontrollable and Minato, as Hokage, might feel it's a threat to the village. He could think that Naruto's power could attract too many dangerous enemies or cause destruction accidentally.
One possible reason could be for the protection of the village in a very extreme and controversial way. Minato might think that Naruto's presence is attracting too much danger and decides to banish him to keep the village safe.
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 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 possible reason could be that Naruto discovers some long - hidden secrets about Minato that he feels betrayed by. For example, if he found out Minato had made a deal that affected Naruto's life negatively in some way, like with the Kyuubi. Maybe Naruto feels that Minato sacrificed him for the greater good of the village without really considering his future or feelings.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
One reason could be guilt. Since Minato wasn't there for Naruto when he was growing up in the original story, in the fanfiction, he might be overcompensating for that lost time. He feels like he has to make up for all those years he wasn't around to protect his son.
It could be that Naruto is trying to prove himself. He wants to show that he can be as great a fighter as his father. Also, he might have received some training or knowledge transfer from someone who knew Minato well. This could have inspired him to adopt Minato's fighting style. He may also be in a situation where his normal fighting style isn't working, so he turns to Minato's as a last resort.
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 Naruto's pent - up anger towards Minato for leaving him as an orphan. He might feel that Minato sacrificed himself without fully considering the consequences for Naruto.