I don't think an honorary doctorate entitles one to be referred to as Dr. In fact, most people with doctorates that I know would rather not be referred to as Dr. In the case of this article, it seems like the author is trying to be overly-formal in the manner of a Keith Olbermann rant.
While I know that the regular practice is to refrain from calling recipients of honorary doctorates "doctor", I think that in some cases it's reasonable. Stallman is definitely more deserving of the title than many "real" Dr.s that you'd find.
Maybe universities need a new class of degree called "honorary doctorate and we mean it for this guy".
