Are we pretending the silk road was actually a legitimate marketplace and a few bad actors might have used it for things that break the law?

It just allowed unrestricted trade outside of regular economy. In a world where the governments themselves are corrupt and criminal, you could argue over the ethicality of the concept. But comparing it to drug cartels is unfair I would say.

He ordered murders. There isn't much of a difference in my eyes.

Sure, but that is a non-sequitur.

It's not necessarily unethical to break the law, merely illegal.

Civil disobedience is a pretty important part of how we have always dealt with bad laws and bad governments.