It can be a very compelling twist. In fanfiction, when Naruto betrays the village, it allows for exploring different aspects of his character. Maybe he discovers some dark secrets about the village leadership that make him question his loyalty. It also creates a lot of room for complex character relationships and intense drama.
Maybe it's to protect the village. He could discover a threat that he can only face away from the Leaf Village, to keep the danger from directly reaching his home and loved ones. He leaves as a form of self - sacrifice.
It completely flips the original story. In the original, Naruto loves the Leaf Village and is willing to sacrifice everything for it. In this fanfiction, his hatred changes the dynamic. It might make his relationships with other characters like Sasuke, who also had issues with the village, more complex.
One possible reason could be feeling betrayed by the village's secrets and politics. Maybe he discovers some dark underbelly of the Leaf Village that makes him lose faith in it.
The village might experience a huge boost in morale. Naruto killing Pain would be seen as a major victory, and the villagers would feel safer. They would look at Naruto as an even greater hero, which could lead to more trust and unity within the village.
It could be due to a prophecy misinterpretation. Suppose there is a prophecy that Naruto misinterprets as the Leaf Village needing to be destroyed for the greater good. Or perhaps he is tricked by a very cunning enemy who convinces him that the Leaf Village is the root of all the problems in the ninja world.
Choji would be sad and also a bit scared. He has always been a loyal friend to Naruto. He might not be as aggressive in trying to stop Naruto as some of the others, but he would try to reason with him, talking about their friendship and how the village has also been a home to Naruto. And Ino would use her mind - related jutsu to try to break any possible mental influence on Naruto if there is one, while also trying to reach out to him emotionally.
The unexpected ally might be a character from a different village, like Gaara from the Sand Village. Gaara has a deep respect for Naruto and has changed his ways after his encounter with Naruto. In this fanfiction, Gaara could come to the aid of the Hidden Leaf Village because he believes that the safety of all villages is interconnected. His unique sand - based powers would add a different dimension to the fight to save the Hidden Leaf Village.
They would probably be highly respected. Naruto is a hero in the Hidden Leaf Village, and if Naruko is also an important figure, their descendants would carry on that legacy. The village would look to them for protection and leadership, just as they did with Naruto.
Their relationship could bring a new sense of unity to the Hidden Leaf Village. If Naruto is Anko's brother, they could combine their skills and influence to make the village stronger. For example, Naruto's charisma and Anko's knowledge of certain ninja arts could be used to train new generations more effectively.