Another possibility is that Naruto was trying to protect someone else from Sasuke. Suppose Sasuke was on a path that would endanger another important character in the story, like Sakura. Naruto, in his eagerness to safeguard Sakura, might have accidentally hurt Sasuke while trying to stop him from taking any harmful actions.
He could be exiled from the village. This is a very severe punishment as Naruto loves his village deeply. Losing the connection with his home and friends would be a great pain for him.
Maybe Naruto gets tired of always chasing after Sasuke. He has his own life and dreams too. He might think that he has sacrificed enough of his time and energy on Sasuke, and it's time to focus on himself and the village. He could start to believe that Sasuke has made his own choices and he can't keep forcing Sasuke to come back.
One possible reason could be his thirst for power. He might see Naruto as an obstacle in his pursuit of greater strength. Maybe he believes that by eliminating Naruto, he can prove himself to be the stronger one and gain more recognition in the ninja world.
A moment of desperation. For example, if one of them is about to die in the alley due to an injury or a curse. The other, in a rush of emotion, kisses them as a way to convey all the unsaid things, all the love and friendship that has been there all along.
One reason could be to create a lot of angst. If Sasuke cheats, it would deeply hurt Naruto and cause a rift in their relationship, which could lead to a lot of emotional turmoil for both characters. This would make for a very dramatic story.
Maybe Sasuke goes too far in his pursuit of power and tries to harm someone Naruto cares about deeply in the Forest of Death. Naruto, in a fit of rage and to protect the person, kills Sasuke.
In a fanfic, it could be for comedic purposes as well. The idea of Sasuke trying to act like Sakura while tricking Naruto can lead to some really funny situations. Maybe Sasuke is forced into this by some strange situation or magic. And he has to keep up the act of being Sakura, which includes mimicking her mannerisms and speech patterns, all while trying to fool Naruto. This could create a lot of humorous misunderstandings and interactions within the story.
One possible reason could be competition. Maybe in this fanfic, they are competing for something like recognition in the ninja world. Naruto, as a female, might feel that Sasuke is getting more attention or opportunities, which makes her jealous and eventually turns into hatred.
One common theme could be the struggle of their friendship. Maybe Sasuke, due to his dark past or thirst for power, ends up physically or emotionally hurting Naruto. Another theme might be Naruto's unwavering loyalty. Even when Sasuke hurts him, Naruto still believes in their bond and tries to save Sasuke from his own darkness. It could also explore the idea of redemption, where Sasuke realizes the pain he has caused Naruto and tries to make amends in the end.
One possible reason could be that it goes against the original dynamic between Naruto and Sasuke. In the original story, their relationship is based on a deep male - male bond of rivalry and friendship. Changing Sasuke to a female might disrupt that established connection.