One possible reason could be jealousy. Maybe Molly is jealous of Hermione's intelligence and the special bond she has with Harry and Ron. Another reason might be that she feels Hermione is a bad influence on her sons in some way. For example, she might think Hermione's Muggle - born status could bring trouble to the family in the wizarding world which is full of pure - blood supremacist ideas.
One possible motive could be jealousy. Maybe Molly is jealous of Hermione's close relationship with her son Ron. Another could be that she feels Hermione is a bad influence on the family in some way, perhaps her non - pure - blood status makes Molly, who has some traditional views, act out. Or it could be a misunderstanding, like Hermione being wrongly accused of something that makes Molly think she's a threat to the family.
Another reason could be related to a prophecy. If there was a prophecy in the fanfiction that Naruto would bring great destruction in the future, and Kushina, being a self - sacrificing mother, might think that killing him is the only way to prevent that destruction, even though it goes against her natural love for her son.
Harry would also be very protective of Hermione. He would likely step in between Molly and Hermione, using his status as the Boy Who Lived if necessary to defuse the situation. He might try to reason with Molly, reminding her of all the good things Hermione has done for them and for the wizarding world.
Molly could have made some inappropriate comments about Hermione's blood status. Even though Hermione is a Muggle - born, she has proven herself time and time again in the wizarding world. If Molly makes a snide remark about her blood, Hermione would surely tell her off for her prejudice.
One possible reason could be that Hermione realizes she has feelings for Ron and wants to avoid any confusion or mixed signals with Harry. She might think that by pushing Harry away, she can focus on her true feelings for Ron.
Perhaps in the fanfiction, there is a plot twist where Sakura has been brainwashed by an antagonist. The antagonist could be using her to get to Naruto, knowing their close relationship. So, she would then be made to attack Naruto without her own will. Or, there could be a prophecy or some sort of pre - determined fate in the fanfiction's plot that causes Sakura to hurt Naruto, even if she doesn't really want to.
It could create a rift in the friendship between Hermione and the Weasley family. If Hermione is hurt, she might distance herself from them. This would be a big change as the Weasley family has been like a second family to Hermione. It would also affect Ron, who is in love with Hermione. He would be caught in the middle between his mother and Hermione, which could add a lot of drama to the story.
One possible scenario could be a misunderstanding. Maybe Molly misinterprets Hermione's actions regarding Ron. For example, if Hermione is being strict with Ron about his studies or his behavior in the fanfiction, Molly, being Ron's mother, might take it the wrong way and say something harsh to Hermione, thus hurting her. Another situation could be related to Hermione's Muggle - born status. If in the fanfiction, there are some rising tensions about pure - blood and Muggle - born wizards, Molly, who is from an old wizarding family, might accidentally let her old - fashioned views slip and make a comment that offends Hermione.
Some Hermione fans might be outraged. They love Hermione and seeing her hurt in such a way, especially by a character like Molly who is supposed to be good, could make them very angry at the writer.
One possible reason could be a misunderstanding. Maybe Molly does something that Harry misinterprets as a threat to his friends or his mission. For example, if Molly tries to keep Harry from a dangerous but necessary task, Harry might see it as her overstepping and feel the need to 'punish' in the context of the fanfiction, which could just be a strong rebuke or some form of isolation within the story's plot.