He might lose his friends at Fairy Tail. Since Fairy Tail is all about friendship and light, joining a dark guild would put him at odds with his former comrades.
The plot could involve Naruto being an outcast in the ninja world after some false accusations. The dark guild offers him a place where he feels accepted. However, the guild's activities are against the values he once held. So he has to decide whether to stay and try to change the guild from within or break away and face the consequences of having associated with them in the first place. It could also lead to some interesting battles where Naruto uses his unique skills against his former comrades who now see him as a threat.
She might lose her friends. In the original story, her friends in Fairy Tail are a big part of her life. If she joins a dark guild, they would likely see her as a traitor. For example, Natsu might be very disappointed and try to bring her back to the right side.
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.
Fairy Tail would be a mix of reactions. The younger members would be thrilled and look up to Naruto as a hero. The older and more experienced members would assess his skills and how he could fit into the guild. They might also be a bit protective of their way of life in the guild at first, but as they get to know Naruto better, they would accept him as one of their own.
In a 'Naruto joins Cross Academy' fanfiction, Naruto would probably be quite confused at first. The setting of Cross Academy is very different from his ninja world. But he'd soon adapt. His combat skills would be a great asset. He could end up teaching some of the students his ninja moves, and at the same time, learn about the unique vampire and hunter world of Cross Academy. It would be an interesting mix of two very different fictional universes.
Naruto would likely be an outlier in the social hierarchy. He doesn't come from the vampire - hunter world, so he wouldn't fit neatly into the existing groups. However, his friendly and outgoing nature might make him popular among some students. He could start his own little group of friends who are interested in his ninja ways.
Some members might be initially cautious. Given her past as a powerful and somewhat feared being, they would be worried about her true intentions. For example, Gray might be on guard until he sees her actions are genuine.
The guild's acceptance of Tiamat would likely be a mixed bag. Some of the more adventurous and powerful members like Gildarts might be more open to having Tiamat around. They would see the potential benefits of having such a powerful ally. However, the younger or more timid members could be very hesitant. They might be worried about Tiamat's true intentions or its power getting out of control.
Naruto would probably fit into the Fairy Tail guild quite well. He has a big heart and is always eager to make friends, which is a common trait in Fairy Tail. His loyalty would also be a great asset to the guild. He could be like the new, energetic member who is always ready for an adventure.