For Sasuke, if Naruto destroyed Konoha, he'd be in a really tough spot. He has his own complex relationship with the village and with Naruto. His goal of revenge against the village would become moot, and he'd have to decide whether to side with Naruto or oppose him for destroying what was once his home too.
One possible reason could be fear. Naruto is extremely powerful, and some in Konoha might fear that he could one day lose control of his power. Another reason could be political intrigue. There may be certain factions within Konoha that see Naruto as a threat to their power and influence. Also, jealousy might play a part. Naruto has achieved so much and has the love of many, and some might be jealous and thus plot against him.
He might initially try to prove his innocence. He'll gather evidence or find people who can vouch for him. But as the situation worsens, he could become angry and more determined to find out the truth and expose those who are behind his false accusation. He might even leave Konoha to seek answers and allies elsewhere.
One possible reason could be a misunderstanding. Maybe some false information was spread in the village that made Konoha believe Naruto had done something wrong. In fanfiction, things can be exaggerated and misinformation can easily lead to a situation of betrayal.
Often, in these fanfics, Naruto discovers a conspiracy within Konoha. Maybe some hidden group within the village is trying to get rid of him because they see him as a threat to their power. So they manipulate events to make it look like Naruto has betrayed Konoha. As a result, Naruto is hunted by the very people he once protected. He then has to use his skills and wits to survive while also trying to clear his name.
One possible plot could be that Naruto's incredible power makes the Konoha elders or some jealous shinobi feel threatened. They might spread false rumors about him being a danger, leading to the village turning against him. Maybe they frame him for a crime he didn't commit, like a powerful attack on the village that was actually the work of an enemy they secretly allied with. This would make Naruto, who has always been loyal to Konoha, feel extremely betrayed.
One possible reason could be jealousy. Naruto is very powerful and some in Konoha might be envious. For example, some minor clans might feel that Naruto, as an outsider in a sense, gets too much attention and resources. Another reason could be fear. His Nine - Tails power is so immense that some might fear he could lose control and endanger the village, so they betray him to try and eliminate the 'threat' before it's too late.
In these fanfictions, it might be related to the secrets Naruto holds. For example, if he discovers something about Konoha's dark past that certain people don't want exposed. They would then try to get rid of him by making him look like a traitor. Also, there could be external forces influencing Konoha to turn against Naruto, like other villages spreading false rumors.
One possible plot could be that Konoha's leaders, fearing Naruto's growing power, secretly plan to get rid of him. They spread false rumors about him, turning some of the villagers against him. Another plot might be that they frame Naruto for a crime he didn't commit, perhaps a major attack on the village, in order to justify exiling or imprisoning him. A third possibility is that they withhold important information from Naruto that could put his life in danger, all in the name of protecting the village's secrets.
Some fanfictions might explore how the main characters, like Naruto, deal with the guilt of not being able to protect Konoha. It could show their journey to regain their strength and find a way to bring back their home.