There could be. Fanfiction allows for a wide range of interpretations and alternate storylines. But it's a really extreme and disturbing concept considering the bonds that Naruto, Sakura, and Sasuke share in the official story. It would be a very different take on the characters, and most fans who love the original story would probably find it hard to accept.
At first, Sasuke might not believe it was Naruto's own will. He would try to find out if Naruto was under some sort of external influence. But if he found out that Naruto was fully responsible, Sasuke's reaction would be one of pure hatred. He would abandon all his previous beliefs and goals and make it his sole mission to destroy Naruto. He might also cut off all ties with the village that Naruto was protecting, seeing it as an accomplice in his sister's death.
One possible motive could be a misunderstanding. Maybe Naruto was tricked into believing that Sasuke's sister was an immediate threat to the village. Another could be that she was somehow involved in a dark plot against Naruto's friends, and Naruto felt he had no other choice to protect them.
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.
This kind of fanfiction usually explores alternate storylines and character dynamics. It might be based on intense conflicts or unexpected plot twists.
If Sasuke's sister was in the picture, Naruto and Sasuke's relationship might soften more quickly. Naruto would see another side of Sasuke through his sister. He might also feel more of a connection to Sasuke's family. Sasuke, on the other hand, would see Naruto's genuine care for his sister, which could make him trust Naruto more.
It could be an original character created just for the fanfiction. Many fanfiction writers like to introduce new characters to add their own unique twists to the story.
It's not a very common trope. Most Naruto fanfictions focus on their friendship or the original storylines. Killing off a major character like 'female Sasuke' (assuming it's a gender - bent or AU version) goes against the essence of the Naruto - Sasuke relationship in the main series which is more about rivalry and redemption. So it's not something you'll see often in mainstream fanfiction.
Yes, there are likely some fanfics out there with such a plot. Fanfiction is a creative space where authors explore different scenarios. However, it goes against the general narrative of the Naruto series where Naruto is more about saving Sasuke.
In Naruto fanfiction, the idea of Sasuke killing Naruto is not overly common but does exist in some darker or alternate universe scenarios. Some writers might explore this to show extreme character development or a drastic change in the story's direction. However, it goes against the core of the original series where their relationship is more about rivalry and ultimately friendship.