Nations will not give up such power freely. They will get in on lyrium, at least the wealthy nations, and set up their own system if the Chantry won't deal with magic anymore.
That's why I say Leliana is only giving mages over to the different nations and will soon destroy any mage unity there is in the south.
Not that I'm against it, but I get the feeling people expect an independent, landless nation like the Dalish which the nations of Thedas gladly hand over resources to like it was some Justice League but with children and elderly.
First of all, is it really a bad thing? I definitely agree that mages without strong Chantry-backed Chicle will end up as being part of their respective homelands to much greater degree they are now. But that's one of the obvious things about freedom of mages: your identity ceases to be based solely on the fact that you are a mage.
Also, we must remember that even before dissolution of old Circle, there were a lot of nation-specific things going on, despite isolation of mages from the society. Particular Circles were already pretty different from one another - think about the Mortalitassi, for example. Pretty much a special national-specific mage order in the very same nation the Circle was centered in.
Despite claims of unity, each nation has its own Chantry and its own Circle, really.
As I said, it creates the precedence of mages in positions of authority. "Magic exists to serve man and never to rule over him" is effectively broken if she becomes Divine.
It does change interpretation of this rule. Since, please do tell me - how is Magic NOT ruling people if being born a mage means that you get extracted from your family and society, forcibly put in an institution enacting strict control over everything you do... and you can't even have a child, since if you do, it's taken away from you right after birth. When you let people's lives to be defined solely by them being touched by the gift of magic - that counts as magic ruling over men in my book.