The debate rages on, but there is a lot of logic, as well as empirical evidence that suggests, at the very least the War on Drugs is, in the nicest light, an immense waste of money, and an increasor of violence. As well as other countries that suggest that drugs being illegal is not best for society (Portugal).
In this case, attempting to shut down Silk Road seems like nothing but trying to police what I do that affects no one else. (In fact, the response to this, "anything can be sold on SR, weapons, etc", feeds back into the problems caused by drugs being illegal).