Well, since al Qaeda's offered a reward for the capture of any American soldier or contractor, it might be worth checking out Mr. Police Chief to see if he's acquired any inexplicable new wealth. And better check out those inlaws and hotel staff, too.
Could his murder somehow be connected to the Iraqi prisoner abuse?
Bingo
That to me seems most reasonable. Also check on if that police chief is Arab or not, though he doesn't NEED to be to be greedy.
You have a Jew with an Israeli stamp on his passport in America. He's detained for fear he's an Israeli spy. Then he's released and eventually captured.
The most likely theory is that someone led AQ to him. All this stuff about him being an AQ-symp because of this email account doesn't make much sense to me.