That's right, he was charged with a "Narcotics Trafficking Conspiracy", with 4 overt acts, a, b, c, and d, and b and c were the murder-for-hire schemes. The overt acts of a conspiracy charge are the guts of the charge itself, and the prosecution has to prove them at trial.

Try this: Google [federal narcotics conspiracy "murder for hire"] (it's not a rare combination of factors!), pull up some DOJ press releases (I found several on the first search results page), and then look them up in PACER. I'm looking at Roger Key (a.k.a. "Luchie")'s 2015 indictment right now, and it's similar. This isn't some weird finagling the prosecutors did with Ulbricht; it's just how you get charged for this kind of conduct.

This notion that prosecutors somehow gave up on the murder-for-hire charge is Internet folklore. It's just not real. What complicated the charge isn't some bungling spy story about the agents involved, but the fact that the murder was a set-up and he didn't actually have anyone killed. But the prosecution established that Ulbricht tried to, and that's also the simplest and most reasonable conclusion to reach given the facts. I've never read an exculpatory explanation of Ulbricht's payment to arrange murders that made any sense at all.