Some writers might use it to explore Sasuke's character in a more extreme way. In the original story, Sasuke has his dark moments, but killing Sakura would be the ultimate act of darkness. It could be a way to show how far he could fall. Also, it could be about exploring the reactions of other characters like Naruto, Kakashi, etc. to such a heinous act.
A possible motive could be a creative exploration of the 'what - if' scenarios. Maybe the writer wants to see how the story would unfold if Sasuke completely lost his way. Another motive could be to create a sense of high - stakes drama. Since Sakura is an important character, her death at Sasuke's hands would be a huge shock.
The motive could also be related to the exploration of power dynamics. Sasuke is a very powerful character. By having him kill Sakura, it shows the extent of his power over her, both physically and perhaps symbolically. It could also be a commentary on the sometimes - fragile nature of relationships in the Naruto world, where even deep bonds can be broken in the face of certain circumstances.
One possible motive could be that Sakura is brainwashed. Maybe an enemy uses some kind of mind - control jutsu on her and she becomes a puppet to kill Sasuke. Another could be extreme jealousy. If she felt that Sasuke was slipping away from her in some way, in a very dark and twisted version of the story, it could lead to her killing him.
One possible motive could be that Sasuke has been consumed by his thirst for power. In the Naruto universe, Sasuke has often been shown to be willing to sacrifice a lot for power. In this fanfiction set in the Wave arc, perhaps he sees Sakura as an obstacle to his pursuit of power, either because she tries to stop him from following a dark path or he believes she will hold him back in some way.
Perhaps in a fanfiction where the world has been completely turned upside down. If Sasuke had been tricked into becoming an unstoppable villain who was about to destroy the entire ninja world, and Sakura was somehow aiding him (maybe under a genjutsu), Naruto might feel he had no choice but to stop them by killing. Another reason could be a broken heart. If Naruto loved Sakura deeply but she constantly rejected him and chose Sasuke, and then Sasuke and Sakura betrayed him in some way, his anger and pain could lead to such a drastic act.
One possible motive could be extreme jealousy. Maybe in this fanfiction, Hinata is insanely jealous of Sakura's relationship with Naruto or her skills, and that drives her to the unthinkable act of killing.
One possible motive could be if Sasuke goes too far in his pursuit of power and becomes a threat to the entire ninja world that even Naruto can't reason with. Maybe Sasuke starts to kill innocent people without hesitation, and Naruto, as the protector of the village and the one who believes in peace, sees no other option but to stop him by killing. Another motive could be some kind of dark magic or mind control that makes Sasuke an uncontrollable force of destruction, forcing Naruto to take drastic measures.
One possible motive could be that Sasuke is so consumed by his thirst for power and revenge that he sees Sakura as a liability or a distraction. He might think that she would try to stop him from leaving the Leaf Village to pursue his own dark path, and in his warped state of mind, decides to eliminate her.
One possible motive could be to use Sakura as bait. Maybe Sasuke is trying to lure Naruto to a certain location. He knows Naruto cares deeply about Sakura, so he figures Naruto will come after her.
Perhaps Fem Sasuke in this fanfiction has a different view of the world. She might believe that Naruto is a threat to her goals or to the future of the ninja world she envisions. It could also be that she has some deep - seated emotional pain that she blames Naruto for, and that leads her to kill him.
One possible motive could be that Sasuke is being controlled by some dark force. Maybe an enemy has a hold over him and is using him to kidnap Sakura as a way to get to Naruto or the Hidden Leaf Village. Another reason might be a misunderstanding on Sasuke's part. He could think that Sakura has some information that is crucial to his personal vendetta and decides to take her by force to get that information.
It could be due to a dark influence. Suppose she was under the influence of some dark magic or an evil force that made her lose her true self and turned her against Naruto. This could lead to her almost killing him in the fanfiction.