Another reason could be that he witnesses corruption or unfairness within the village leadership. If he sees that the system is rigged against certain groups, including himself or his friends, he could grow to hate Konoha and decide to leave.
Some people create such fanfiction maybe because they like to explore alternative or dark storylines. They might think it's interesting to deviate from the canon relationship between Naruto and Hinata.
In fanfiction, the evidence often lies in the way the author portrays Naruto's interactions. For example, Naruto may be shown being cold or dismissive towards Sakura, like avoiding her company or not showing any romantic interest. Meanwhile, with Hinata, he could be depicted as being more affectionate, like blushing around her or always coming to her aid. But it's important to note that this is all in the realm of fan - created interpretations and not the official canon.
The story would deviate from the original themes of unity and friendship. Naruto's hatred could split Konoha into factions. This would mean different training regimens, different missions, and different loyalties. For example, Naruto might start his own group of ninjas who share his views, which would completely change the power dynamics in 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.
There could also be political reasons. Some factions within Konoha might have seen Naruto as a tool or a threat to their own political power. His influence and popularity could have disrupted the existing power balance, leading to animosity from those who wanted to maintain the status quo.
One possible reason could be that it goes against the original essence of Naruto's relationship with Konoha. Naruto has a strong bond with Konoha, and yaoi fanfiction might distort that relationship in a way he wouldn't like. Another reason could be that Naruto is a character who values traditional values and friendship in a non - sexualized way, and yaoi fanfiction often sexualizes male - male relationships which he may find inappropriate.
Perhaps Naruto discovers some dark secrets about Konoha that go against his values. Like if the village has been involved in unethical practices that he can't overlook. This could be things like using underhanded tactics against other villages, which would make Naruto, with his strong sense of justice, turn against Konoha.
One possible reason could be for the sake of creating a more complex love triangle in fanfiction. Maybe the writer wants to explore a different dynamic where Naruto and Hinata's relationship is strengthened by having a common dislike for Sakura. It could also be that the fanfiction writer is trying to give Hinata more agency and make her a stronger character by having her oppose Sakura in some way, perhaps in matters related to Naruto's affections.
It would be a huge blow to Konoha. Naruto is a hero in the village, and his departure would leave a big leadership void. The villagers would also lose a great source of inspiration. Hinata is from a respected clan, and her leaving would also have an impact on the clan's standing in the village. Morale among the ninjas might drop as they see two important figures leave.