I can't say I know every detail of the case but I don't recall anyone getting killed or even hurt by Mr. Ulbricht so in my mind the punishment does not fit the crime. IMHO the death penalty should be off the table completely (go Nebraska!) and life in prison reserved for only violent offenders. You can argue that he enabled people to harm themselves but I think that's stretching it. If people want to take drugs, even take too much drugs their going to get it somewhere. If drugs were legal and treatment of abuse the focus instead of punishment Silk Road wouldn't have existed in the first place.
I think it's pretty much impossible to run that kind of a global darkmarket otherwise. Even if you were the world's most experienced sysadmin and could lock down your server(s) (and NSA/FBI httpd/nginx/apache 0day doesn't apply) you still have to worry about Bitcoin laundering and many other issues, you'd have to run around like Jason Bourne everyday and nobody can sustain that discipline without making mistakes. You only have to make one mistake and you're joining Ross at ADX Florence (where he's likely going, nobody convicted of the "Kingpin" charge ends up anywhere else besides supermax prisons)
However, that would not be so easy for hundreds or thousands of Bitcoins. It's hard for a snake to discreetly swallow a pig. Numerous wallets and small transactions would be prudent. But the process could probably be automated.