Well, you’re half correct. He was charged in Maryland for attempted witness murder, but the charges were dropped once he’d been sentenced so harshly in New York. The reasons for this are not entirely clear, and there’s plenty of conspiratorial debate about them.

I strongly doubt that the prosecution would have brought the charges if they didn’t have traceable evidence (through blockchain transaction records, undercover police chat logs, and data seizure) that coins, sent to an undercover agent for the purposes of murder, originated from wallets that were owned by Ulbricht. You can read more about one of the employees Ulbricht allegedly tried to have murdered (Curtis Green, who was sentenced for his own crimes) here and here.

You’re right, though, he’s technically innocent as the charges were dismissed. Perhaps it was all a huge setup/honeypot but the truth of whether or not he sent the coins should be discoverable with enough due diligence scouring the blockchain records. Intent matters, even though it didn’t end up getting tried in this instance.