It's a tough call. The silk road had a 'harm reduction' ideology associated with the site. The problem is it's impossible to know if it was successful in this way. Does buying drugs online make you safer? I think you could make an argument for that. Does buying a gun online make you safer? I think there are arguments both ways here.
One thing the Wired article in the post explores, along with the original silk road philosophy, is the shadier sites that sprang up after the shutdown in 2013. It appears that there was a certain level of 'trust' built up in the silk road community that has evaporated. The new sites have no real overarching philosophy, they're just profit driven.
Am I avoiding your question...perhaps I am. I don't know the answer, but what I do know is that if people want something badly enough they will find a way to get what they want. They don't need the internet. Shutting down these sites is not going to solve anything. Legalizing drugs, after decades of a failed 'war on drugs' would probably do more to reduce harm than anything else i can think of.