Naruto would probably be conflicted. On one hand, he has a deep love for Konoha, his home. But on the other hand, he might have been hurt by the past events that led to his departure. He could initially be hesitant, but eventually be swayed by the thought of seeing his friends again.
He would probably be very angry. Naruto has always been a free - spirited person, and being experimented on against his will would be a huge violation of his rights. He might initially try to resist physically, but as the situation gets more complex, he could start to plot his escape and revenge.
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.
At first, Naruto is likely to be heartbroken. Konoha has been his home, and he has always longed for acceptance from the villagers. So being abandoned would be a huge blow to him.
Sakura would probably be very worried. She has always cared about Naruto deep down, so she might be constantly trying to find a way to bring him back. Kakashi, on the other hand, would likely understand Naruto's reasons to some extent. He might be sad but also respect Naruto's decision. As for Sasuke, if he is in the village at the time, he could be conflicted. He and Naruto have a complex relationship, and Naruto's leaving might make him realize how much Naruto actually means to him.
Sasuke might be more understanding. Given his own experiences of leaving Konoha, he could respect Naruto's decision. However, he might also secretly plan to keep an eye on Naruto from afar to make sure he is safe.
In some fanfics, Naruto initially tries to reason with the people of Konoha. He believes that there has been a misunderstanding and he wants to clear his name. But when he realizes that no one is listening, he becomes angry and frustrated. He might start to lash out at those who are hunting him.
Naruto might initially try to reason with those who betrayed him. He would want to understand why they did it. But if they refuse to listen or continue to be hostile, he would start to distance himself from Konoha. He could become a lone wolf, using his skills and power to survive on his own while still trying to figure out how to clear his name and get revenge if necessary. He would also likely feel a sense of betrayal towards the friends he thought he had in Konoha.
Naruto would likely be extremely hurt. He has always considered the Konoha 11 as his friends and comrades. So, at first, he would probably be in denial, trying to figure out what went wrong. He might try to talk to them, to understand their reasons.