It's very clear that they were trying to get him in prison ASAP in order to make an example of him, and so they fixed the whole process. I think that he will probably get released eventually due to the mountain of process violations and the fact that he was only convicted of non-violent crimes. Maybe in the end he'll end up spending less time in prison than if he'd taken the plea bargain.
As an anarcho-capitalist, I believe that there was nothing unethical about the Silk Road. That said, I think that the whole freedom-fighter angle is a bit of a stretch. If I wanted to be an anti-government activist by means of a darknet site, I'd:
1) Recognize that current anonymity tech is extremely weak, and maintain a constant samurai mindset of "I'm already dead / in prison".
2) Not make any money from the site. This would allow the site to be more effective, it'd make detection much more difficult, and it'd be a bit of a defense in court.
If you do drug transactions, intentional tax evasion, etc., then I feel like you're mainly just trying to make money, and the idea that it's not unethical (which I agree with) and is a form of civil disobedience is just something that you use to deceive yourself into thinking that it's a good idea when in reality it's just an extremely stupid way of trying to make money. If you want to fight for freedom, pick a better hill to die upon IMO.
On the murder-for-hire accusation, it's important to remember that he was never convicted of that, and AFAIK nothing like that was a part of the Silk Road site. Though I have some non-public info which makes me slightly more inclined to believe the accusation, and if it's true, then that's completely unethical, of course. (Not worth 2 life sentences, though.)
BTW, has anyone read Curtis Green's book about this?
It's weird how they're trying to point fingers at Mark Karpeles. I really doubt that he had any involvement.