It has already been stated that the Juubi can be injured by being hit by it's own TBB.
Madara's War Fan got the ability to deflect TBBs.
Naruto is the only one with enough chakra to wield one of the Sage's Weapons. Which it most likely is.
By stealing the War Fan they could wound the Juubi or atleast be guaranteed that no more TBBs would be fired.