There's a lot of stuff I'm still trying to figure out as well--both of those points you raise are still open questions. The Federation's conduct in this matter, too, is something I'm still trying to work out. So far, all I know is that as they did with the Bajorans in the canon universe, they know what's happening to the Cardassians, but they aren't intervening on a large scale even by 2370.
The role of Cardassia is also something I'm still trying to figure out. Now that I've written the Pah-Wraiths and something
in direct opposition with each other at AU Dukat's behest...it may be that in their universe there's a third player involved, separate from the Prophets and Pah-Wraiths (or at least that has a much more active role than in the canon universe). But, I'm still not entirely sure.