Another factor could be the toll it took on his mental health. The ANBU often deals with dark and difficult missions. Naruto, with his positive and somewhat naive outlook on life, might have been affected more than others. He could have started showing signs of not being able to cope, and as a result, they forced him out to protect him from further harm.
One possible reason could be the intense and often dark nature of Anbu missions. Naruto might be exposed to a lot of death and destruction, which could lead to his depression. For example, he could witness the killing of innocent people during a mission and feel powerless to stop it.
In some fanfictions, Naruto might leave the Anbu due to internal conflicts within the organization. There could be corruption or power struggles. Naruto, being the idealistic character he is, would not want to be part of such a messed - up system. He might have discovered some dark secrets about the Anbu that made him decide it was not the place for him.
If Naruto's friends or loved ones are threatened by the ANBU, either directly or indirectly. For instance, if the ANBU's actions put Sakura or Kakashi in danger without just cause, Naruto would be likely to turn against them. He's very loyal to his friends, and any threat to them would be a strong motivation for him to take action against the ANBU.
At first, Naruto might be angry. He's put in a lot of effort to get into the ANBU and prove himself. So being forced out would feel like a slap in the face. He might go on a rant about how unfair it is.
Another reason might be related to their different ideologies within the ANBU. Naruto may have believed in a more collaborative and friendly approach within the organization, while Sasuke might have been more focused on individual achievement and power. This fundamental difference could lead to Naruto hating Sasuke in the fanfiction.
One possible reason could be a conflict of power. Naruto has his own set of powers from the Naruto universe, like chakra and jutsus. In Fairy Tail, magic is the main power source. Maybe his powers were seen as a threat or too different, causing the guild to force him out. For example, if his chakra-based attacks were disrupting the magical balance in Fairy Tail's world.
One reason could be political. Maybe the two clans or villages that Naruto and Sasuke are associated with want to strengthen their alliance. By marrying their most powerful members, they hope to ensure peace and cooperation.
Perhaps there is a threat that Kakashi has detected, and he believes the best way to keep Naruto safe is to take him out of the village. It could be a group or an individual who is specifically targeting Naruto within the village, and by leaving, they can avoid this danger and also work on finding a solution to deal with the threat on their own terms.
One possible plot could be Naruto retiring from the ANBU due to the toll it has taken on his mental and physical health. He might then focus on mentoring the next generation of ninja in Konoha, sharing his unique skills and experiences.
In fanfiction, Naruto and Anko Anbu could have a mentor - mentee relationship. Anko, being an experienced Anbu, could teach Naruto some of the more stealthy and darker aspects of the ninja world that he might not learn otherwise. Maybe she'd show him some unique jutsu or how to better handle dangerous missions.