Unfortunately there is a huge distance between what libertarian philosophy argues for and what is actually legal. To me, Silk Road is a no-shit-it's-completely-illegal enterprise given the current war on drugs. Plus, it's a major thumb right into the drug enforcers eyes. Not smart if you care about staying out of jail.
Should we change the laws? Absolutely. But this guy was not doing anything to change those laws. He was just profiting from the situation because he was willing to take the risk (or dumb enough to take the risk). I don't find him especially sympathetic. If he was out there saying 'I run Silk Road, and we are not responsible for what people are doing on it', or even better 'I run Silk Road, and we are eliminating violence from the drug trade, it's a net benefit to society by eliminating gangs', he would be someone worth defending. It would be a lot harder for the state to come down on him. Maybe some people would rally behind him and demand change because he is right. Instead, I'm just seeing a guy that made a lot of money by violating laws, and wants to dodge the consequences right up until he is thrown in jail.