I doubt the higher ups ever disagree with the hokage when it comes to that. Sarutobi also chose Minato over Orochimaru. I doubt the elders were happy with that.
Even if some super ninja nations was created I doubt every village will file under 1 Kage, let alone the Hokage. Makes no sense, if they are going for peace. You also seem to be forgetting the villages work for the nations. Why would all the nations give up their individual sovereignty?
I'm pretty sure everything will go back to as it was, but with a super treaty that somehow prevents all out wars or the entire village system would have to be abolished.
I understand your position. But this is an idealist manga, which is why I hold my position. Kishi has shown in the past the problems of politics in the pursuit of peace. In the end, getting rid of the politics, borders, and everyone holding hands is how I'm willing to bet he'll represent peace.
The other variable is that both Naruto and Sasuke are the only demigod level characters in the entire world at the end of all of this. They will have the power and influence to change the world in the end, especially since Naruto has been prophesied to do this. But, there are many variables to discuss in this scenario that haven't happened yet, so it is hard to discuss the ends and outs of both of our positions.
But I doubt the end result of Nations and Villages will be very realistic, and will lean much more towards idealistic.