Maybe for shock value. Some writers want to create a story that stands out and goes against the norm. By having Naruto kill villagers, it's a huge deviation from the original story and can grab readers' attention.
Perhaps the writer has a different view on the concept of justice in the Naruto world. They might think that the villagers' treatment of Naruto was so bad that in their version of the story, Naruto takes revenge. But this is a very extreme interpretation. In the original story, Naruto chose forgiveness and a path of positive change, not vengeance against the villagers.
One possible reason could be fear. Naruto has the Nine - Tails inside him, and the villagers might be so afraid of the power of the Nine - Tails getting out of control that they decide to take extreme measures. They might see Naruto not as a person but as a potential threat that needs to be eliminated.
One possible reason could be mind control. Maybe an enemy uses a powerful genjutsu on Naruto, making him lose control and attack the villagers. For example, Orochimaru might have a new jutsu to manipulate Naruto's mind for his own evil purposes.
One reason could be years of built - up resentment. The villagers have treated Naruto poorly for so long, constantly shunning him and making him feel like an outcast. In fanfiction, this could reach a boiling point where he just snaps. For example, if someone in the village made a particularly cruel comment about his parents, it might be the last straw.
One possible reason could be fear. The villagers might be afraid of Naruto because of the Nine - Tailed Fox sealed within him. They see him as a potential threat and lash out in their fear. Another reason could be jealousy. Naruto is a powerful ninja in the making, and some villagers, who are not as strong or talented, might take out their insecurities on him.
One possible reason could be the way the villagers treated him as a child. They ostracized him because he was the host of the Nine - Tails. He was often alone and looked at with fear and disdain, which could have gradually built up his hatred.
Some writers might be influenced by other dark or violent media and try to incorporate those elements into the Pokemon fanfiction world without realizing how much it goes against the essence of Pokemon. Or perhaps they are just trying to be edgy and different, thinking that writing something so out - of - the - ordinary will make them stand out, but in reality, it's just in bad taste.
One possible reason could be extreme guilt. Maybe he fails to protect his friends in a major battle and feels so responsible that he can't bear it. For example, if Sasuke were to die because Naruto couldn't reach him in time, Naruto might sink into such deep guilt that he sees no way out but death.
Some creators might want to explore a darker side of Naruto's character. Maybe they're tired of the always - positive and heroic Naruto and want to see what he'd be like if pushed to the extreme.
Some people might create it just for shock value. They want to get a reaction from the Naruto fan community by presenting such a radical and against - the - norm idea.
One reason could be to explore a different side of Naruto. Maybe the writer wants to show how even a character as positive as Naruto could break under extreme circumstances. Another reason might be to create a more complex and less idealized version of Naruto.