It might be a rogue ninja from the Wave. They could have a vendetta against Konoha and see Naruto as an easy target to frame and cause chaos between the two places.
Maybe a corrupt official within the Wave. They want to get rid of Naruto because he's getting too close to uncovering their illegal activities, like embezzling funds meant for the village's reconstruction after the initial Wave arc events. So they stage his betrayal.
There's also a chance that it's an unknown force that has infiltrated the Wave. They have their own agenda, and Naruto's presence in the Wave is a hindrance to them. So they manipulate the situation to make Naruto look like a traitor to both the Wave people and his own comrades.
Obviously, Kami would be the main antagonist. Since the title says 'naruto betrayed by kami', Kami is the one doing the betraying, which makes him the bad guy in this fanfiction.
Another possibility is that there is a false god or a demon that has influenced the true gods to betray Naruto. This false entity could be the real mastermind behind the whole situation. It wants to use Naruto's downfall to gain more power or to bring chaos to the ninja world. So Naruto not only has to deal with the betrayed by the gods part but also has to uncover the true source of this conspiracy which is this false god or demon.
The main antagonist could also be a corrupt official within the Wave Country itself. After the events of the first mission, this official could have risen to power and now has plans to use his position to gain more control, even if it means going against Konoha. He could be secretly working with other villains or using his own resources to create problems for Naruto and his friends.
It could be Xehanort. He's a powerful and devious character in Kingdom Hearts. If he sensed Naruto's power and saw him as a threat, he might engineer a situation where Naruto is made to feel betrayed. Xehanort could manipulate the events and the people around Naruto to make it seem like his new friends in the Kingdom Hearts world are against him, all so that he can either eliminate Naruto or turn him to his side.
It could be a new character, someone who is jealous of Naruto's growing power and popularity among the girls. This person might spread false information to turn everyone against Naruto. Maybe a rogue ninja who has infiltrated the village and has a vendetta against Naruto for some unknown reason.
It could be one of the powerful and corrupt prison guards. They might have their own hidden agendas and see Naruto as a threat to their power or secrets within the Blood Prison. So, they start a scheme to make it seem like Naruto has betrayed everyone.
The Jedi Council themselves could be the main antagonists. Since they are the ones betraying Naruto, they would be the ones he has to oppose. Their actions of betrayal would drive the conflict in the story.
It could be the very villagers who once looked up to Naruto. Their betrayal could turn them into antagonists as they might try to further harm Naruto to protect their own interests.
Danzo could also be the main antagonist. He is known for his underhanded methods and distrust of anyone with too much power. Since Naruto has the power of the Nine - Tails, Danzo might spread lies within Team 7 to make them think Naruto is a danger, causing them to betray him.
It could be Zabuza. He might pretend to be on Naruto's side at first during the Wave events and then betray him when Naruto least expects it. Zabuza is a mercenary and his loyalty can be easily swayed.