If a Mafia boss never strong armed a merchant, never busted any kneecaps, and never pulled a trigger but simply paid other people to carry out various crimes, should the law give him a short sentence because he was non-violent?

I don't know what the appropriate sentence for Ulbrecht, but I think your claims about proportionality are missing the fact he didn't just direct commit a few crimes, such as trying (unsuccessfully) to hire a hitman, but he facilitated hundreds of thousands of crimes. Maybe you think selling drugs and guns to randos should not be illegal, but that is a separate question of whether or not he broke the laws as written.

As for your last point, I don't disagree that the wealthy/powerful/connected live under a different justice system than everyone else.