It could be due to a perceived betrayal. Suppose Naruto discovers some dark secrets within his family that he can't overlook. In his 'godlike' state, he might be more morally rigid and thus decides to disown them. For instance, if he finds out that his family was involved in some unethical ninja practices in the past, he would feel compelled to distance himself.
The plot could develop with Naruto creating his own new 'family' of sorts. He might gather like - minded ninjas who understand his vision. For example, he could team up with ninjas from other villages who also strive for a new kind of ninja world order.
It could also be due to a rift in their relationship over Boruto's ninja path. If Boruto decides to take a very different and unorthodox approach to being a ninja that Naruto doesn't approve of, such as using forbidden jutsu without proper understanding, Naruto might disown him in the fanfiction.
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.
In the context of this fanfiction, Naruto's family might banish him because they don't fully understand his 'godlike' powers. They see the surface level of his new strength and assume the worst. Maybe they think he has been corrupted by some unknown force. Also, it could be related to power politics within the family. Some members might see Naruto's power as a threat to their own position and influence, and so they convince the rest of the family to banish him to safeguard their own interests.
It could also be due to some external influence. Perhaps an enemy manipulated Naruto's mind in the fanfiction, making him see his family in a negative light. This enemy might have used some form of mind - control or false memories to turn Naruto against his family.
It could also be related to external forces. Maybe an enemy of the family or the village plants false evidence that makes Naruto seem like a danger. Since he is 'godlike', the family might believe the false accusations more easily, fearing his power, and expel him. Also, there could be a power struggle within the family, and those in power see Naruto's 'godlike' nature as a threat to their authority and use some excuse to kick him out.
One possible reason could be a sense of being too powerful and outgrowing the team. If Naruto in the fanfiction has become 'godlike', he might feel that the training and missions of Team 7 are no longer challenging enough for him. He may seek greater challenges elsewhere.
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 a dark magic influence on James Potter in the fanfiction. Maybe he's been cursed or possessed, causing him to act out of character and disown Harry.
One possible reason could be fear. Naruto's 'godlike' powers might be too much for the village to handle. They could be afraid that he might accidentally cause destruction. Another reason might be envy among some of the villagers or ninja. They may not like that Naruto has become so powerful all of a sudden and want him out of the way.