Most probobly a payment to a merchant would be made with partially tainted and partially clean bitcoins. As time goes on more and more transactions each would have a small amount of taint in them. And we are supposed to do something about this?
This is exactly how real world cash works as well. I bet some of the cash in your pocket (if you have any) has at once time been either stolen, used for drugs or other illegal acts. Cash is that way.
The goal isn't to attack the tainted funds, the goal would be to trace the transactions to hopefully, eventually lead back to the identity of the thief such that he can be found out and be punished / sued in a civil suit. With cash, it's harder to trace the order and how the transactions took place. However, like mentioned, the thief would have to inadvertently give himself away in some fashion by tying multiple of his addresses to his real identity. This would provide sufficient evidence for law enforcement to act.
We need to protect our private property rights. However, like any free market, I'm fairly certain a solution will evolve to deal with this. I'm just trying to put some ideas out there in the hopes that somebody adopts the cause.