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.
Perhaps there is a prophecy or some ancient power at play. Naruto discovers that by sacrificing the Konoha ninjas, he can save the entire ninja world from a much greater threat. He is forced to make this tough choice, knowing that it will make him an outcast, but believing it's for the greater good.
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.
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.
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 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.
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.
It could be a result of a prophecy misinterpreted. He might believe that destroying the ninja villages is the key to fulfilling some grand prophecy that he thinks will ultimately lead to peace, not realizing the true meaning of the prophecy which has been distorted by false information.
Well, it could be a dark corruption of power. Maybe in this fanfic, the 'god' power Naruto obtains warps his mind. He might see his family as a threat to his new - found godly status, fearing they'd try to stop him from using his power in certain ways.