Clemency petition for Ross Ulbricht reaches 7,000 signatures in less than 4 days

>The charge of procuring murder was removed from the indictment[31] although the evidence was factored into Ulbricht's sentence.

The transcripts aren't just evidence of murder, also of his direct involvement with the drug vendors.

He's been imprisoned for amongst other things, "continuing criminal enterprise", and the transcripts of him talking about hits were presented at trial as at evidence that this involved preparedness to take extreme measures to protect his narcotics suppliers comparable to those of drugs kingpins, and not simply being an innocuous libertarian-inclined middleman who built a web platform people chose to buy and sell drugs on, or even your friendly neighbourhood pot-grower. His defence team had the opportunity to challenge the validity of that evidence in determining his guilt and sentencing for the crimes he was charged for and evidently did not succeed in doing so. The difficulties with targets being mostly anonymous (and in some cases possibly nonexistent) and the pseudonymous entity who offered supposed hitman services probably intending to scam Ulbricht might have made a prosecution for five specific instances of murder too uncertain to complicate the case with, but as evidence of Ulbricht's willingness in principle to purchase murders was it certainly relevant to the continuing criminal enterprise charge he was convicted of.

The only thing the authorities decided they could certainly convict Al Capone for was tax evasion. This did not mean that Al Capone was unfairly treated, it simply meant the tax charge were relatively straightforward to make stick.

I feel like judicial discretion in sentencing is pretty well understood, but I guess it could seem strange if you haven't spent much time reading about or experiencing the legal system.

Sentencing is a range. Based on the facts presented to the judge during trial and through third parties in the sentencing phase (victim statements, letters from your pastor, parents, friends, and teachers, etc.) judges can choose the low end of the range or the high end of the range. It's no more strange to give someone the high end due to unproven statements of assholerly, than sentencing being more lenient for good qualities that have never been proven.