The issue is not that he holds such views, the issue is that he brings it up in the context of free software in order to push the line "the gummint is out of get us", which makes it a little unpalatable to many.
I agree it's not effective rhetorically. Digging into any controversial issue is rhetorically risky for a public figure. What is worrying to me is the disproportionate sensitivity Americans have to this particular bit of controversy. All he said is he believes the US government was involved in 9/11. He didn't say how or in what capacity. Yet based on many of the responses, you'd think he said that Lizard Man Bush flew the planes himself by remote control. The author complains that Stallman is marginalizing himself, yet if he and others are willing to attempt to marginalize him based on unpopular (not crazy) political opinions, who's really to blame?
