I think you are misconstruing the author. He supports the right to have an anonymous exchange. That an anonymous exchange makes it possible to hide illegal activities is unfortunate, but unavoidable, in his view. This is similar to the common opinion that encryption software should not be outlawed just because it can also be (and is) used to hide evidence of crimes.
I agree that it's strange to say this isn't up for debate (I don't think there is anything that isn't up for debate and this exact point is being debated all the time). The article seems to be a reiteration of the author's beliefs on the issues of privacy and drugs, to which Silk Road is only tangentially relevant.