Perhaps in the fanfic, the female Kyuubi convinces Naruto that Konoha is corrupt and has been using him all along. She might show him some hidden secrets of the village that make him believe that Konoha doesn't deserve to exist. Also, it could be that Naruto is forced into a situation where he has to choose between the female Kyuubi (who he has some sort of bond with) and Konoha, and he chooses the former, leading to him taking drastic action against the village.
One possible reason could be that the female Kyuubi has some sort of mind - control over Naruto. Maybe she has her own vendetta against Konoha and uses Naruto as a tool to carry out her revenge. Another reason might be that Konoha has done something extremely unforgivable in the eyes of Naruto, like harming the female Kyuubi in a cruel way that makes Naruto snap and turn against the village.
In this kind of fanfic, it could be that the female Kyuubi represents a different ideology or power that is in conflict with Konoha. Naruto, being influenced by her, starts to see Konoha's flaws in a new light. Maybe the village has been suppressing certain powers or groups that the female Kyuubi stands for. Naruto, in his idealistic way, decides that the only way to bring about change is to destroy the current system of Konoha, which unfortunately means killing the village itself.
Another possibility is that he wants to explore the world outside Konoha on his own terms. Naruto has always been curious, and in a fanfic, he might decide that he can't be tied down to one place. He could be on a quest for self - discovery, believing that Konoha's environment is limiting his growth.
In some fanfics, Naruto might leave Konoha as a child because he feels ostracized. Since he's the jinchuriki of the Nine - Tails, many villagers fear and shun him. He could get tired of the constant cold shoulders and decide to leave in search of a place where he'll be accepted.
Yes, there might be such fanfics. One possible reason could be exploring alternative storylines. Writers might want to break the traditional view of Naruto's loyalty to Konoha to create more complex and unique plot twists. For example, they could be imagining a scenario where Naruto discovers some dark secrets about Konoha that make him question his loyalty.
Maybe there are some dark secrets within Konoha that he discovers in the fanfic. These secrets could be related to the treatment of certain individuals or something more sinister about the village's leadership. Discovering such things could make Naruto decide to leave in order to distance himself from the corruption or unfairness.
One reason could be if Sasuke was somehow possessed by a powerful and evil force during the Chunin Exams. Naruto might see no other way to stop this threat and be forced to kill Sasuke to protect the village and others. Another possibility is a huge misunderstanding. For example, if Sasuke was framed for a crime he didn't commit and Naruto was misled into believing he was a danger.
I'm not sure if there is such a specific fanfic. There are countless Naruto fanfics out there, but a plot where Naruto kills Konoha is quite a dark and unorthodox one. It might go against the general themes of the original series. However, the world of fanfiction is vast, and it's possible that someone has written such a story with a female Kyuubi element.
Maybe in a fanfiction where Kakashi is mind - controlled. It could lead him to harm Naruto without his normal self - control.
One possible reason could be that Naruto feels betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him lose faith in it. For example, if he finds out that the village elders were involved in unethical experiments or plots against his friends or family, he might not want to help.
Naruto might forgive Konoha because he realizes that holding a grudge won't solve anything. He has seen the destruction that hatred can cause, like during the Pain arc. So, he chooses to forgive in order to move forward and bring about positive change. Another reason could be his respect for the previous Hokages and their ideals for Konoha.
One possible reason could be that Konoha has made decisions without considering Naruto's opinions. Maybe they have made policies that Naruto believes are unjust towards certain groups, like the treatment of the Uchiha clan in the past. Naruto, who values fairness and friendship, would be angry at such insensitivity from his village.