Actually, he took over in March of 2005. IIRC he probably would have been relieved either late this year or early next (anything over 36 months as a CO is HIGHLY unusual).
Damn, this sucks. Dude was on my first boat when I was a lowly non-qual as well. He really was one of the good guys. That sucks.
The D.C. suburbs, and elsewhere, are filled with good military people who caught an unlucky break.