Some of Harry's friends could also be antagonists in this fanfiction. They might not understand his reasons for wanting to destroy the wizarding world and try to stop him. For example, Hermione, with her love for knowledge and the wizarding world's institutions like Hogwarts, would probably try to reason with Harry and, if that fails, might even fight against him to protect the world she loves.
It could also be a story where Harry has lost all hope. He has seen too much death and destruction in the wizarding world, from the war with Voldemort. He might think that the only way to end all the pain and suffering is to just end the wizarding world as it is. He could start by attacking the key institutions like Hogwarts and the Ministry of Magic.
There would be shock and disbelief. The wizarding world has always seen Hogwarts as a symbol of hope, knowledge and safety. If Harry destroys it, many would be in denial at first, thinking it couldn't be true. Wizards and witches from all over would come to the ruins, trying to figure out what had happened.
Another possibility is that there could be a new character introduced in the fanfiction, a mastermind who manipulates Harry into believing that his family is a threat. This new character could be the main antagonist.
It could be a new dark wizard we haven't seen in the original series. Maybe someone who has a vendetta against Hogwarts and manipulates Harry into doing the dirty work of destruction.
Some would be in shock and disbelief. People who idolized Dumbledore would initially refuse to believe Harry's claims. They would think Harry was either misinformed or had some malicious intent.
The Order of the Phoenix members might also back Harry. They've fought against the dark forces before and if they see that the Ministry has become a threat, they'd side with Harry. Dumbledore's old allies in the Order would believe in Harry's judgment and join him in his mission to destroy the corrupt Ministry.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
It could be one of the headmasters or organizers of the Triwizard Tournament who has a hidden agenda. They might be using the tournament for their own gain, perhaps to gain power or wealth, and Harry's actions to destroy it are thwarting their plans.
Some pure - blood supremacist wizards could be antagonists. They don't like the idea of Harry creating a haven for all kinds of wizards on the island. They might try to sabotage the island's creation or attack it once it's made, fearing that it will disrupt the 'purity' of the wizarding bloodlines.
The remaining Death Eaters could be the antagonists. Even though Voldemort is gone, there could be some who still hold a grudge against Harry and want to finish what their master started. They might track Harry and Ginny down as they run away, creating dangerous situations for the couple.