Orochimaru would likely be a main antagonist even if Naruto joins the Sound Village. Orochimaru has his own devious plans, and Naruto might not fully agree with them. Even though Naruto is in the village, Orochimaru could try to use Naruto for his own gain, like getting access to the Nine - Tails' power. So, Naruto would constantly be at odds with Orochimaru.
The main antagonist could be an external force. For example, another village might see Naruto joining the Sound Village as a threat. They could send their own ninja to either kidnap Naruto or destroy the Sound Village to prevent it from getting stronger with Naruto's help. This external village's ninja would be constantly causing trouble for Naruto and the Sound Village, making them the main antagonists in the fanfiction.
Another possibility is an external force, like a neighboring village. They see Naruto and Yugito joining the new village as a threat to their own power. So, they send spies or launch small - scale attacks on the new village in an attempt to drive Naruto and Yugito away. They might also try to turn the new villagers against Naruto and Yugito by offering false promises or by spreading lies about their intentions.
One plot could be that Naruto is captured by the Sound Village. Instead of being treated as an enemy, they try to convert him. They show him their training methods and how they are building a strong village. Naruto, being the curious and empathetic person he is, starts to understand their motives. He begins to think that by joining them, he can bring about change from within. So, he decides to stay and become part of the Sound Village, while still holding onto some of his Konoha values.
Perhaps an old enemy of one of the members of Team 9 shows up. Since Naruto has joined the team, they might see it as an opportunity to get revenge. This antagonist could be someone who was once defeated by the member's family and now wants to prove themselves. They would be very cunning and use their knowledge of the team member's past to try and divide the team.
It could be an old enemy who has resurfaced, like Orochimaru again. Since Naruto and Sasuke are together now, Orochimaru might see them as a threat to his own plans for power and immortality.
It could be the leader of the dark guild. This person would likely have a very different ideology from Naruto's. Maybe the leader believes in using extreme and unethical means to gain power, like sacrificing innocent lives for dark magic. Naruto would constantly clash with this leader as he tries to uphold his own values.
Orochimaru could still be the main antagonist. Even if Naruto joins Team Hebi, Orochimaru's motives are often self - serving and evil. He might be using the team for his own experiments or to gain power, and Naruto would oppose that. Naruto's presence in the team could disrupt Orochimaru's plans, leading to a conflict between them.
It could be a rogue hunter nin who doesn't like the idea of Naruto, an outsider, joining their ranks. This rogue hunter nin might see Naruto as a threat to their power and influence within the group.
It could be the ninja from Naruto's former village who don't want him to succeed in his new place. They might see his new - found influence as a threat and try to undermine him.
It could be a rogue ninja from his own village who wants to use Naruto's unique position (being from a different village but having ties to the Leaf through his adventures) to start chaos. This ninja might be jealous of Naruto's popularity and abilities, so he tries to frame Naruto for various crimes to turn the different villages against him.
It could be a rogue ninja who has mastered a forbidden jutsu and wants to destroy the village out of revenge. Naruto would then have to face this extremely powerful foe and in the end, sacrifice himself to stop the destruction.