I think you've possibly misinterpreted the argument the author is making. My interpretation wasn't that he was being critical of the FBI for shutting it down; of course they had to shut it down. Rather, the criticism is of the laws and policies that are in place which dictate that the FBI had to shut it down in the first place.

As the article notes, law enforcement has been given a "hopeless task", where if you subscribe to the view that Silk Road actually made buying and selling drugs safer (as I do), shutting it down has made the whole business less safe at direct risks to citizens of many countries. As you note, the FBI had to do this, but it's a huge indictment of our drug policy that this is the action they are compelled to take given the result.

Which brings us back to the war on drugs...