The Pains are already dead, remote controlled zombies. Even Jiraiya made the mistake of thinking they would die just like any normal dudes, only to have them backstab him later. A single rasengan, while dangerous to normal humans (except in fillers), should do little to a zombie.

However, I think his point was the fact he managed to save Ebisu. Assuming they have enough wits to escape now. Or burn the body to ashes while it's still unmoving - assuming they possess a sufficient jutsu.