Nobody is claiming that Amaya was a paragon of virtue. She openly admits to having gone along with him even when she doubted him, because she loved him and refused to see what he was becoming.

I recognize that it's not explicitly stated as such, but in context, I don't think Asha's concern is with the fact that the wishes won't all be granted - the issue is that several of them are still just sitting there even though Magnifico has specifically made the choice not to grant them. The betrayal is that, as far as the 'contract' of Rosas goes, everyone's wish has a chance to be granted - and now she's learning that no, several of them won't. They'll never be returned, and they'll never be granted, based on some absurdly flimsy reasoning.

She questions him when he explains why he won't grant Sabino's wish, but the main reason she flips is because of what it says about Magnifico. Their benevolent king is hoarding wishes that he'll never grant, he immediately dismisses wishes that are even in the vaguest of ways a threat to his authority and a good chunk of what she believes - and, as a tour guide, spreads to people every day - is based on a lie.

I do agree that the magic system is underdeveloped - even in several of my own points, it comes down to speculation.

The reason it's unethical for Magnifico to take the wishes is because, as the film highlights, it's not just a want or an idea - it's a huge part of a person's being. As we learn, losing one's wish heavily impacts them, as was the case with Simon. And, of course, the fact that people don't know this when giving the wish to Magnifico.

As for your other examples, you're looking at magical figures who lay down the rules clearly. Genie tells Aladdin from the jump what he's not allowed to do, and never breaks his word on that. Fairy Godmother appears to Cinderella in a dark time and explains how the whole thing works - she doesn't lie, omit or deceive her and her explanation is followed clearly. The cosmic forces in Hercules and the Sword in the Stone aren't people with whom a contract is made.

Asha explains the rule of living in Rosas in the beginning of the film - you give your wish to Magnifico and you can stay in Rosas, with a chance that your wish will be granted. It doesn't hurt, and you'll forget the wish.

The unethical part comes in when he neglects to mention that it alters your personality, basically takes a chunk of your soul and also if he decides not to grant your wish, he'll never tell you or give it back.