He used a clone as a distraction against Kakuzu, so couldn't he do that again without using sage mode?
The Rasenshuriken was originally told to be off-limits due to the physical damage inflicted by its use. Because Naruto used it like a traditional Rasengan, which requires that the jutsu make direct contact with the enemy, the damage done to his person couldn't be avoided.
The reason that a clone could not work in this scenario would be due to the fact that clones are dispelled once sufficiently high physical damage is inflicted to it. It would be my belief that a clone could never sustain its form long enough to sustain a hit with the Rasenshuriken before it - and the jutsu - were dispelled.