Any metaphysical claim can be used to create a "power over" relationship

But not every metaphysical claim is. There are plenty of metaphysical beings even in European mythology who aren't tyrants or even leaders of anyone. Jormungandr is terribly powerful, but he doesn't rule the world, he just eats it. He doesn't oppress anyone until Ragnarok. And it's not just because he's an animal. The Dryads aren't out here building empires, they just want to be left alone with their trees. Cú Chulainn is a supernaturally good warrior with the Hulk's superpowers, but he doesn't oppress anyone. In fact, when he kills Chulainn's dog, he offers to be the man's hound until he finds a new one. That's humility and respect for other people.

The gods were created by people. And people create gods that match what they see in life. Life is good and life is bad. Gods are good and gods are bad. Gods will be worse in a more oppressive culture, and gods will be better in a less hierarchical culture. There's no doubt that the culture of the people who enslaved the world is worse than the culture of their victims. It's not "noble savage" thinking to say that. It's not that people who don't have kings are better than "normal" people. People who don't have kings ARE normal people. Living in a feudalistic or capitalist society is weird and bad. Anarcho-communism is the way humans naturally live.

And besides, the Mayans gave the Europeans a run for their money in the "sucking and having authoritarian gods" department.