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.
The disowning could also have an impact on the other characters. For instance, Hinata might be caught in the middle, trying to reconcile Naruto and Boruto. The other villagers might have different opinions about the situation. Some might side with Naruto, believing he had a good reason, while others might think Naruto is being too harsh on Boruto. This can add layers of complexity to the fanfiction's plot.
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.
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.
Maybe it's the high expectations that Naruto has for Boruto. Naruto is a hero, and he might unknowingly put a lot of pressure on Boruto to follow in his footsteps. Boruto could be scared of not being able to meet those expectations.
Perhaps Boruto disrespects the ninja way that Naruto holds so dear. In fanfiction, Boruto could be shown as being too rebellious, and Naruto, as a firm believer in the ninja values, would snap at him to correct his behavior. For example, if Boruto were to shirk his training or mock the importance of teamwork, which are fundamental to Naruto's view of being a ninja.
Perhaps in fanfiction, Boruto is associated with a group or ideology that Naruto opposes. This could cause Naruto to view Boruto unfavorably. Also, if there are false rumors or misinformation spread in the fanfiction world about Boruto, Naruto might believe them and start to hate Boruto until the truth is revealed. And sometimes, it's just a way for the writer to make an interesting and unexpected plot twist.
It could be that the fanfiction simply doesn't meet Boruto's standards for what the Naruto universe should be like. He has grown up in that world and has his own ideas about how things should be. Fanfiction can be very hit - or - miss in terms of quality and faithfulness to the source material. If it's of poor quality or changes things too much, Boruto might hate it.
One reason could be Boruto's recklessness. In fanfiction, Boruto might engage in dangerous stunts or actions that go against Naruto's teachings. For example, if Boruto were to use a forbidden jutsu without fully understanding the consequences, Naruto would be angry as it not only endangers Boruto but also those around him.
Some fanfictions might explore the idea of Naruto being betrayed by someone close to him. This betrayal could lead to a situation where he is caught off - guard and killed. It adds a dark and dramatic twist to the story.
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.