I don't have much of an opinion on the specifics. I discovered the darknet just last summer and most of the interesting and dubious things had already happened. I presumed the guilty verdict was a forgone conclusion.
From your podcast analysis it seems that the defense was not allowed to provide appropriate expert witnesses, which is sorta lame.
Cynically speaking I think its in everyone's best interest to let the whole Silk Road thing sorta die its own quiet death. The collective consciousness seems to be willing to let the BC=DRUG TRAFFICKING connection fade to obscurity. Right or wrong, not talking about the injustice of it all seems to be the best course of action if we are to find a path to a more peer to peer future ;-)