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.
One possible scenario is that Naruto starts to learn new and unique jutsus from Itachi. Itachi is highly skilled, and he could pass on some of his knowledge about the Sharingan and powerful genjutsu. Naruto, with his determination and Itachi's guidance, might become even stronger, and they could form a plan to deal with the threats to Konoha that they both know exist.
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 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.
It could lead to political unrest in Konoha. There might be those who blame the village leadership for Naruto's departure. This could lead to power struggles as different factions try to take control and change the way the village is run. Some might demand more transparency and better treatment of their shinobi to prevent such a thing from happening again.
Konoha's power structure could be affected. Naruto is one of the strongest shinobi in the village. Without him, the village might be more vulnerable to attacks from other villages or threats. They would need to quickly find ways to fill the gap in their defenses.
Sasuke might be more understanding. Given his own experiences of leaving Konoha, he could respect Naruto's decision. However, he might also secretly plan to keep an eye on Naruto from afar to make sure he is safe.
It could create a sense of unease and fear. Naruto is a very powerful ninja, and if he turns dark and leaves, the villagers would be worried about him coming back as an enemy. It might also lead to a decrease in morale among the ninjas who once considered Naruto a friend or ally.
Well, perhaps Naruto could be framed for a crime in Konoha and then be forced to leave as an assassin. He might start working for an enemy village at first, but then gradually realizes that there's a deeper conspiracy behind his framing. So he decides to clear his name and also protect Konoha in the end.