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.
Still, IMO it is reasonable to bring that up as a character issue.
In general, entrapment is when the police convince you to commit a crime that you wouldn't have committed otherwise. So, if you want to kill your wife, and your friend (FBI agent) happens to say one day, "Hey, I do a little killing on the side, just for gits and shiggles," and you hire him, that's not entrapment.
In contrast, if the agent is manipulating you and saying, "Hey, your wife is going to divorce you and take your stuff. Killing her is the only way to prevent ruin" and slowly convincing you to do it, then that's entrapment.
Bottom line: Already predisposed to doing the crime and probably would have gone through with it if it hadn't been the police? You're screwed. In contrast, if you're normally completely innocent and the person has to convince you to commit the crime, it's entrapment.
I suspect it's more likely they wanted to convict him on just the SR charges because that's better publicity, but it’s still odd.