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.
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.
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.
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.
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.
Ron would probably be horrified. He loves Hermione deeply, and his mother has always been an important figure in his life. He would be caught in a really difficult situation. He'd likely try to stop his mother immediately and protect Hermione.
Well, sometimes in fanfiction, authors like to explore dark and twisted ideas. Maybe they want to create a contrast to the kind Molly Weasley in the original series. It could be a way to add drama and conflict to the story, even if it's a bit out of character for the Molly we know.
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.
Maybe in this fanfiction she experiences a great loss, like the death of a loved one in a very tragic way. For example, if Ron or Harry were killed in a battle and she blamed herself for not being able to prevent it. This overwhelming guilt could be a reason for her to try to kill herself.
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 that she might think Harry is putting himself in unnecessary danger, like when he goes off on his own to face Voldemort without a proper plan. Molly is very protective, and she may feel frustrated with Harry's recklessness.