Tobi isnt the bad guy. He wants peace for everyone and that´s the only way to get peace... maybe he has to kill some people but when you want real peace there has to be some sacrificing...
Naruto cant do anything about peace! People will still hate eachother, he cant control the whole world... there will always be hate and love = ying yang principle
That´s my view of Naruto and Tobi.
Do what you have to do!