Let's get back to basics: FBI is supposed to enforce the laws. They do have some leeway in prioritizing, but a $1.2 Billion market is way too big not to attract enforcement.
Now about the war on drugs...
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...
I got his point correctly, that's why I said it isn't up to the FBI to choose a safer way for people to buy/sell drugs. That it's not their mission. Congress of course can change the laws
The main difference in my eyes is that the DoJ is ultimately not worried about Colorado or Washington doing something "crazy" and legalizing all drugs, because they're part of the U.S. and ultimately dependent on the federal government. Silk Road was independent and sizable, and thus a threat.