He isn't doing it all just for Rin, he's trying to create a world where people don't have to make pathetic excuses. It's more about creating this fantasy world of his where everyone is forced to live in peace. It's just as easy to look at Naruto as the villain. Rather than letting Obito create a world filled with peace, he's fighting for the sake of the egotism of the villages and their oppressive, backward and undemocratic rule. A naive child, he's simply fighting to protect his community and failing to see the bigger picture.
It's perfectly arguable that from a moral standpoint, Naruto is the bad guy in this situation. Just another pawn of a corrupt system. I doubt that's where Kishi is going with this, but Obito doesn't want to just avenge Rin. He isn't Sasuke, he's much older and more mature about things. He sees the implications of war and of letting someone like Madara get his way.
The key to understanding Obito is that he's given up on the reality of this world. He wouldn't bring Rin back to such a horrible and rotten place. It seems like he's trying to convince Naruto to give into despair and join his side, rather than killing him outright. It's pretty obvious that with the power of the Juubi he could just target Naruto the person and slaughter him easily. Then there's Madara. Right now the Alliance is at a serious disadvantage.