What people should be more concerned with is the fact that the government is selling off someone elses property before they have even been convicted of a crime. Dread pirate roberts plead not guilty and has still not had a trial yet. He has not been convicted of any crime so if these are his coins they are selling them before the trial is even finished
Civil forfeiture is not confiscation of your property as punishment for committing a crime. It's a determination that the property was never yours to begin with, because it was obtained in an illegal transaction.[1] That's why the standard for civil forfeiture isn't whether the person is guilty "beyond a reasonable doubt" but rather whether the property is the fruits of a crime by the "preponderance of the evidence." Any civil dispute over the rightful ownership of property is evaluated according to a preponderance of the evidence standard, and the dispute about the status of the property can be resolved without resolving the issue of criminal guilt.
The very important distinction to make here is that the issue of whether Ulbricht is guilty is distinct from whether the money is the proceeds of illegal activity. Maybe Ulbricht gets acquitted because he creates enough reasonable doubt that he isn't DPR, as he claims. Or because he succeeds in getting key evidence excluded because of a procedural failure by the feds. His acquittal doesn't mean that the money wasn't the product of illegal activity. Indeed, he has tremendous incentive to try and prove that he never owned these Bitcoins, because that goes to proving he isn't DPR!
[1] At least when we're talking about cash. There's a whole host of more questionable issues when it comes to things like forfeiture of vehicles and guns used in crimes. See: http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1459...; see also: http://ij.org/pennsylvania-judge-calls-civil-asset-forfeitur... (for a particularly egregious example).