Admiral Boorda appears to have been arcancided for not being a Clinton yes-man. Boorda's incompatibility with that administration was his integrity. The SNAFU with the medal seemed more of a Clinton-driven media attempt to tarnish the man's sterling reputation.
I believe that Boorda was the type to speak the truth, get the job done right, and then let the chips fall where they may. IOW, a sure-fire way to be marked for death in certain unsavory circles.
From everything I have read, the man was a sterling U.S. patriot.