It's in their best interest to keep racing him. The Breeder's Cup Classic is a $4 million dollar purse. There's plenty of big races leading up to that also - the Haskell, Travers, etc.
Even as banged up as Funny Cide was after the Triple Crown races last year, they still found a way to get him running in the BC Classic. As long as Smarty Jones stays healthy, they have to keep going with him.