One possible motive could be that Minato is under some sort of dark magic or mind control. In fanfiction, authors often play with the idea of characters being forced to act against their true nature. So, if Minato is being controlled, he might end up doing something as extreme as killing Naruto.
Maybe in this fanfiction, Minato believes that by killing Naruto, he can save the village from a greater threat. He might have been misled to think that Naruto will become a dangerous entity in the future and that sacrificing him is the only way to prevent a catastrophe.
A possible motive could be that Naruto discovers some dark secret about Minato that makes him feel betrayed. For example, if he finds out that Minato was involved in some unethical experiments that led to the suffering of many people. Or perhaps Naruto is tricked by a powerful villain who manipulates his emotions and convinces him that Minato is the root of all his problems.
Perhaps Minato has been corrupted by power. In the fanfiction world, he might have come across some source of power that has twisted his mind. By sealing Naruto's chakra, he could be trying to take that power for himself. It could also be related to some prophecy that he misinterprets. He thinks sealing Naruto's chakra is the key to saving the world, but in reality, it's the opposite.
One possible motive could be a misunderstanding. Maybe Haku was disguised as someone else who was about to attack Naruto or his friends, and Naruto reacted in self - defense without realizing it was Haku. Another could be that in this fanfiction, Naruto has been somehow corrupted or influenced by a dark force that made him lose his normal judgment and attack Haku.
It could be that his siblings have made a pact with an extremely evil entity. Naruto, with his sense of justice and loyalty to the greater good, decides that their existence in that state is too dangerous and kills them, though it would be a very difficult and heart - wrenching decision for him.
Another reason could be related to a prophecy. There might be a prophecy that Boruto will bring great destruction in the future, and Naruto, as the Hokage, feels it's his duty to prevent this at all costs. He might think that by killing Boruto, he can change the course of fate and protect the people he loves and the entire ninja world.
It might be an exploration of the 'nature vs. nurture' concept. Writers could be interested in seeing how Naruto's character would develop if he had a negative influence like an abusive Minato instead of the loving father he was supposed to have. Also, some might do it just to be different from the mainstream fanfictions and explore a more edgy side of the Naruto universe.
It could also be due to a misunderstanding. Suppose Naruto accidentally does something that Kurama misinterprets as a threat to its own existence. For example, if Naruto tries a new jutsu that Kurama wrongly perceives as an attempt to suppress it further.
One possible motive could be mind control. Maybe an enemy used some powerful genjutsu on Naruto, making him lose his true self and turn against the Uzumaki clan. It's a common trope in fanfictions where the hero is forced to do something unthinkable.
One possible motive could be that the angel attendant was working for an enemy force that Naruto perceived as a threat to his village. So, in order to protect his home and the people he loves, he might take such a drastic step.
One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.