Another reason could be a very dark and alternative interpretation of the characters. Maybe the writer has a different view of Naruto's character arc and how he could be pushed to the extreme. And they see Sakura as a character that could be sacrificed in this extreme version of Naruto's story. But this is a very far - fetched view considering the original story's development.
It could also be a result of a plot twist in a complex and convoluted fan - created storyline. The writer might be trying to explore the limits of the Naruto universe and the characters within it. However, this type of fanfic is likely to be controversial and not well - received by most Naruto fans who are more attached to the positive and friendly relationships depicted in the original series.
It could be because of a dark power corrupting Sasuke. Maybe an ancient evil force takes over him and makes him see Sakura as an enemy. In some fanfics, this kind of external influence can completely change a character's actions. Also, it might be related to Sasuke's pursuit of power. If he believes Sakura is standing in the way of his ultimate power - seeking goal, he could be driven to kill her.
Maybe in a very dark and twisted fanfic, Naruto could be possessed by some evil force. This would override his normal sense of self and his love for his friends, causing him to harm them.
One possible reason could be a sudden and extreme corruption of Naruto's character. Maybe he is influenced by some dark and powerful force that makes him turn against his friends. Another reason might be a misinterpretation of a prophecy or some kind of mind - control situation.
One reason could be for the sake of creating drama. Writers might want to explore how the Naruto universe would be shaken up by such an event. It could also be a way to explore different character aspects of Naruto and Hinata that aren't shown in the original, like how Naruto would react to such betrayal.
One possible reason could be mind control. Some dark power might take over Naruto's mind and force him to turn on Jiraiya without his own will.
It could also be that Naruto is forced to leave Sakura due to some external threat or danger. For instance, if there is an enemy targeting Naruto and he fears that being around Sakura will put her in harm's way, he would choose to leave to keep her safe. This is in line with Naruto's selfless nature as seen throughout the series.
In some fanfics, Naruto may ignore Sakura because he has his own emotional traumas to deal with. He might find Sakura's presence a reminder of things he wants to forget or move past, so he chooses to keep his distance. For example, if he has faced a lot of rejection from her in the past, he could decide to just cut her out of his life.
Some fans might create such a disturbing fanfiction as a form of extreme dark - themed exploration. They may want to break away from the typical love - story - esque nature of the 'Twilight' series and create something that shocks and stands out.
One reason could be betrayal. If the council betrays Naruto in some way, like selling him out to an enemy, he might kill them in retaliation.
Some people might create such a fanfic just for the shock value. They want to break the norms and create something that is completely different from the original story. It could also be that the author has a very different interpretation of the characters' relationships and is exploring a very extreme 'what - if' scenario.