Excellent theory, well constructed and contains great research and comparision of characters =D
I enjoyed reading it a lot because it makes sense and is logical. There is very high probability that Kishi will do that =D
However I don't like this idea personally

. Evil side in this war is already very thin in compare to Alliance Shinobi Army:'(. If even Obito leave evil side, then only Madara and Juubi will be left.
Idk about Madara, maybe Hashirama will talk no jutsu him to return to good side or disappearing
However Juubi will become perfect, absorb Gyuuki and Kurama, then maybe after seeing Alliance efforts (even although Naruto and Killer bee will be dead, lost hope) Juubi will see huge change in humankind, no corruption, no hate and besides that everyone united to work together for their Greater good. There is only way I see Juubi to forgive humankind or give them second chance as it walks away or dissapear with giving them last warning before walking away.
This warning would: 'Know my mercy. I give you humans second chance to live in peace and don't destory nature. However !!, If it reapear and hate, corruption and another bad emotions return then I will defnitely destroy humans and this time noone will be able to stop me"
That my thoughts about your theory and this topic in general =D