Jiraiya might also side with Naruto. Jiraiya has always been a mentor and a father figure to Naruto. He would believe in Naruto's innocence and help him. He could use his connections and knowledge to keep Naruto safe and help him clear his name.
Sasuke could potentially be an ally. Given their complex relationship, Sasuke might understand Naruto's situation and choose to side with him. They have a deep bond, and Sasuke has also been an outcast in a way. Another could be Jiraiya. If he were still alive, he might believe in Naruto's innocence and help him from the shadows.
Kakashi could also end up being an ally. Despite his loyalty to the village, if he discovers the real reasons behind Naruto's departure and realizes that the village has made a mistake, he might choose to help Naruto secretly. He has a deep bond with Naruto and would not want to see him in harm's way.
Sasuke could potentially be an ally. Since they have a complex relationship, Sasuke might understand Naruto's situation and choose to side with him against the village. Also, characters like Jiraiya could still believe in Naruto and help him from the shadows.
In such a fanfic, it could be that Naruto discovers some dark secrets about the village leadership. These secrets are so dangerous that the leaders try to silence him. Naruto refuses to be silenced and decides to break away from the village, becoming a missing nin. He then travels the ninja world, gathering allies who also believe in exposing these secrets and fighting against the unjust system of the village.
In a 'naruto becomes a god fanfic', Naruto's allies could include not only his friends from Konoha but also some unexpected characters. For example, some of the tailed beasts that he has befriended over the years might become his allies in a more direct way. They could combine their powers with Naruto's new god - like abilities to face common threats. And perhaps some of the old ninja clans that have respected Naruto's power and his ideals would also side with him.
Kimimaro could be an interesting missing nin character to explore in fanfiction. He was a tool for Orochimaru, but had his own internal struggles. You could write about his life before fully becoming a missing nin, his loyalty to Orochimaru despite his own deteriorating health, and what might have happened if he had broken free from Orochimaru's control. Another character could be Nagato. Before he became Pain, he had experiences that could be considered as leading towards a missing - nin - like existence. His views on peace and his use of the Akatsuki could be delved into in the context of a missing nin story.
In a 'naruto becomes a missing nin fanfiction', perhaps Naruto discovers some dark secrets about the village leadership. These secrets are so dangerous that the village wants to silence him. He then decides to go rogue to expose these secrets to the world. As a missing nin, he might form alliances with other outcasts who also have a grudge against the current system.
Isolation is a common theme. Since they are missing - nins, they are often alone and have to fend for themselves. Another theme is redemption. Many of these fanfics explore the idea of the missing nin trying to make up for their past mistakes.
Sasuke could be one of his allies. Despite their past differences, Sasuke would recognize the potential of Naruto's new power and the good it could do. Also, Kakashi could be an ally. His wisdom and experience would be valuable in guiding Naruto in this new role. And of course, the other members of the Konoha 11, like Sakura, who would support Naruto in his journey as a god of destruction, believing in his good intentions.
Naruto's personality would likely become more patient. As a medic nin, he would need to be calm and focused during treatments. His impulsiveness would probably decrease as he realizes that any hasty move could harm a patient. He might also become more empathetic, understanding the pain and suffering of others on a deeper level.