Well, it could be that Naruto, with his godlike powers, leaves Konoha because he feels misunderstood. Maybe the villagers still fear his power despite all he has done for them.
Perhaps he discovered some dark secrets about Konoha that made him lose faith in the village. For example, if he found out that the village leaders were involved in unethical or immoral activities that were against his values, it could make him hate Konoha. He might also feel betrayed if his so - called friends turned their backs on him for some reason.
His 'godlike' status might make him more aware of the flaws in Konoha. He could see through the power structures and politics that normal villagers might not notice. This awareness could fuel his hatred as he realizes how unjust the system in Konoha is.
Sasuke could be involved. He might either try to stop Naruto from leaving, believing that they should face whatever comes together in Konoha, or he could decide to join Naruto on his journey, as they have a deep bond.
Konoha would initially be in shock. Naruto is a hero to many in the village, and his sudden departure with Itachi, who was once considered a traitor, would cause a lot of unrest. The villagers might start to question the leadership of the village, wondering why Naruto left and if there was something they could have done to prevent it.
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.
One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
Another reason might be that Naruto is seeking a greater purpose. In the fanfiction, his 'godlike' state could make him realize that there are threats out there that he can't face while being tied to Konoha. He may leave to protect the world on a larger scale, believing that he can be more effective away from the village.
One possible reason could be to seek stronger opponents outside of Konoha. Naruto might feel that he has outgrown the training opportunities in the village and wants to face greater challenges.
This type of fanfiction concept is really out of the ordinary. Naruto's character is built on his values of friendship, loyalty, and his dream of becoming Hokage. Killing Sasuke would mean betraying all of that. However, in a fanfiction, the author might be exploring the 'what - if' scenario. For example, what if Sasuke's actions against Konoha were so heinous that Naruto felt he had no choice? But still, it's a far - fetched and very different view from the original Naruto we know.