He could have been part of a second-wave bio or chem attacks, something the govt. has been very reluctant to elaborate about, not unlike their touchiness about labeling any post-9/11 airline incidents with terrorism, a bow to the airline lobby IMO. Naming Hatfill as a "domestic" perp also gave a false sense of security - a sole actor, wrapped up with innuendo who is no longer a danger in the future.
M's case might implode the various Fed dissembling - moving him to a secret tribunal reinforces might be motivated by avoiding this uncomfortable eventuality.
The al Qaeda operatives under detention are enemy soldiers, captured behind our lines and out of uniform, in violation of the Geneva Convention.
It shows incredible weakness that any of them are still alive, much less that we are quibbling over details of the trial.