Perhaps in a very dark and alternate Naruto universe, the power of some dark entity corrupts Naruto. This entity could twist his values and make him see his sister as an obstacle to achieving some ultimate power or goal. It could also be a situation where there's a time - travel paradox or a change in the timeline that alters Naruto's personality so drastically that he becomes capable of killing his sister.
If such a fanfiction exists, one possible reason could be a mind - control situation. Maybe an enemy uses some powerful genjutsu to make Naruto believe his sister is a threat, causing him to kill her accidentally. Another reason could be a misinformation plot where Naruto is tricked into thinking his sister has committed some unforgivable crime against the village.
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 possible reason could be a miscommunication that escalates out of control. Maybe Sasuke is on a path that Naruto believes is too dangerous for the world, and Naruto, in an attempt to stop him, accidentally kills him. For example, Sasuke might be about to use a powerful and uncontrollable jutsu that Naruto fears will destroy the Uchia compound and much more, so he acts in haste.
Yes, such fanfictions exist. In these fictional scenarios, Naruto might kill himself because of Sasuke for several reasons. Naruto's whole life has been centered around Sasuke to some extent. If he feels that he has failed in his mission to bring Sasuke back to the right path and that the situation has become so dire that the only way to atone for his 'failure' is through his death, he might do it. Also, if Sasuke were to cause harm to someone Naruto holds dear, like the village or his other friends, and Naruto feels powerless to stop him in any other way, he could choose to end his own life as a last resort.
Some writers might do it just for shock value. They want to create a story that stands out by being extremely controversial.
Power imbalance could also be a reason. If Naruto's power suddenly goes out of control or he misjudges the Teen Titans' power levels and thinks they are a danger to his world or friends, he might take extreme actions. For example, if there's some kind of power - up in Naruto that makes him overly confident or paranoid, he could lash out at the Teen Titans thinking he's protecting something important.
One possible reason could be that the council has been secretly plotting against Naruto all along, perhaps trying to undermine his power or even get him exiled. Naruto might have discovered their malicious plans and decided to take pre - emptive action to protect himself and his friends.
It could also be due to a misunderstanding. In the heat of the moment during the vote, there might have been miscommunications or false assumptions. Naruto might have thought Sasuke was going to betray them all and in his haste to prevent that, made the tragic decision to kill him.
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.
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.
One possible reason could be a misdirected spell during a battle. In the heat of a fight, Harry's spell could go awry and accidentally kill Malfoy. Another reason might be if Malfoy was under the control of a dark wizard and was about to do something truly terrible, and Harry had to stop him at all costs, including taking his life.