While I have a lot of sympathy for aaronsw, and admired a lot of the work he did, I don't see a lot in common between the two.
The Feds. charged both, but the thing is that the charges brought against aaronsw were largely absurd. He appeared to have broken a few misdemeanor-class laws, but was charged with wire fraud and the CFAA in ways that didn't really fit what he did at all.
The Feds. are charging Ulricht with things that he mostly was personally responsible for. He very much appeared to be engaged in narcotics trafficking conspiracy, continuing criminal enterprise, computer hacking conspiracy, and money laundering conspiracy. He set up an environment where people can freely transact with one another, but tailored that environment to narcotics trafficking, credit card fraud, selling malware, and money laundering, and chose to engage in tailoring the site specifically for those things. He was fully aware of the illegal transactions occurring through his site and not only did nothing to stop it, but enabled it and profited from it. He was also hit with a Kingpin charge that probably will stick, since he was personally involved and managed an organized crime scheme.
The Silk Road designed a site for drug trafficking and other illicit activities, recruited drug and encouraged dealers, and took a commission from the sales. Since the Feds. have the server they have a sea of evidence to show how the site wasn't running with no knowledge of what transactions were happening, but tailored itself to be effective at drug, CC, and malware trafficking.
Whatever you think morally about profiting off drug deals, malware sales, CC fraud, and money laundering, the law is really clear about it.
aaronsw was engaged in a kind of hacktivism that expanded open access to public information and contributed to the open web in many ways. Ulricht was engaged in making a profit by opening a marketplace for illegal activities and tailoring it for drug deals. There's a world of difference.