Well maybe he should have been charged for that.
To be clear, though, the judge did still explicitly permit the murder-for-hire evidence to be submitted during trial, even though he wasn't charged for it. They also factored it into the sentencing.
When I say "most critical part", I mean from a moral standpoint, especially for people who see no moral issue with drugs. For the government, the drug kingpin stuff was enough to build a case. For libertarian-sympathizing people who otherwise would've supported him, the murders-for-hire are what change this from something worthy of protest to something pretty open-and-shut.
Ulbricht should be grateful none of the murders actually happened as the CCE has a special clause for murders carried out as part of operating the criminal enterprise, making the defendant eligible for the death penalty. Contract murder is quite serious because of the huge amount of premeditation involved (i.e. not a "crime of passion" or temporary misjudgment) and cold-blooded motives such as money or concealing other criminal activity.