DA_MILK
In an interview Arakawa explained that alchemy existed before father and that most of the nations practiced it. With time the concepts and beliefs changed and Father moulded the people— taught the countries with no alchemy. Places like Ishval took the hits of time and their people with new beliefs appeared like those fanatics that consider Alchemy evil and against the teachings of god. The ones that followed the ancient forms went into hiding and despite the people hating them, they remained loyal to the country. The latter part is from a forum and not Arakawa as she never explained the reasons behind it. The first part is canon the latter one is based on theories. But she did say that she might explain if she ever made side stories... this will include Mustang becoming Führer, the history of the nations etc.