He might be mind - controlled. Some dark magic or an evil character could take over Naruto's mind and force him to act against the ponies in the MLP world.
If Naruto is trying to protect his own world. He could believe that the ponies in the MLP world are a threat to his world, Konoha. So, in order to safeguard his home and the people he loves there, he might be forced to take actions that would be considered betrayal in the MLP world.
A misunderstanding could lead to his so - called betrayal. Naruto may misinterpret the actions or intentions of the ponies. For example, if he sees them gathering a large amount of magic, he might think they are planning something bad and take pre - emptive actions against them, which would seem like betrayal to the ponies.
One common reason could be that he finds out the village has been using him all along. Maybe they were only interested in his power as a jinchuriki and not really in him as a person. This realization could lead to his betrayal.
A reason could be that Sakura says something really hurtful to Naruto about his dreams or his abilities. Naruto, who has always been sensitive about those things deep down, might lose his temper and punch her.
It could be that they were misled. For example, they might have been tricked into believing that Naruto was a threat to the village in the future. So, in an attempt to safeguard the village they love, they decided to 'betray' Naruto. This would add a lot of complexity to the story as Naruto discovers the truth later.
Some authors may write it to add a new dimension to the Naruto universe. Naruto has a huge fan base, and by exploring such a taboo topic, they can attract readers who are interested in seeing a different side of the character. It could also be a form of creative exploration, to see how the story and other characters would react if Naruto were to reach such a low point in his life.
Sometimes in fanfiction, the plot demands a big twist. So the author makes Annabeth betray Percy to shock the readers. It could be a completely out - of - the - blue reason like she suddenly decides she doesn't like Percy's friends and since he won't abandon them, she betrays him.
A dark magic - using villain from the MLP universe could also be the one to betray Twilight at the wedding. This villain might have infiltrated the wedding planning under a false guise. They could then use their magic to turn Twilight's friends against her during the wedding, making it seem like Twilight has done something wrong when in fact she is the victim of betrayal.
It could also be related to some hidden family secrets or prophecies. Maybe there was a prophecy that Naruto would bring great destruction in the future and Kushina, believing in it, thought she had to stop him before it was too late. This would be a very complex and heart - wrenching betrayal if it was based on such a false premonition.
In some fanfictions, Ginny might be written to betray Harry because of a prophecy. The prophecy could mislead her into thinking that Harry was going to bring doom, and so she decides to act against him to prevent that. It's a different way of looking at their relationship compared to the original story, where their bond was based on love and trust.
One reason could be a power struggle. If there was a rare and powerful Pokémon at stake, Ash might be tempted to betray Korrina to get it for himself. In the Pokémon world, power and rare Pokémon are highly coveted.
Power could be a reason. If there's a chance for Ron and Hermione to gain a great deal of power by turning against Harry, some fanfictions might explore this. For instance, a new dark power might offer them something they've always desired, like the ability to reform the wizarding world in their own image. They might think Harry would oppose this, so they betray him to get what they want.