Obito will have a change of heart, when he finds out that Madara was behind it all
If you pardon the pun :snick:
But anyway, it now appears Obito knows how Rin died, and that he started the war because he's fed up with the shinobi system (which is a lot more understandable, since it shows that villages will go very far to win a war).
However, it's still plausible that Madara was behind the order to kidnap Rin. Isn't it a bit of a coincidence that out of aaaaaall the people the Mist shinobi could've chosen, they went with Rin... exactly when Madara needed Obito to be converted for his plan? The bloody mist had also started before Obito went evil, so most likely someone else was behind it.
I think that Obito won't be convinced or TnJed by anyone, but will actually decide on his own to bring down Madara with the help of Naruto. Perhaps it will be temporarily co-operation, in a "the enemy of my enemy is my friend" type of deal... or it will be a way to completely bring Obito on Kakashi's side.