Saddam Hussein's organization survives (hanging on), as does Abu Musab Zarqawi's. The death of Osama bin Laden if he were dead (applies to Zawahiri) would not bring about the demise of his organization, in fact, many argue his death would strengthen Al-Qaida (I am doubtful an organization that can not protect its leader is not worth joining).
So, I am seeing said some criticism is being leveled against Operation Phantom Thunder and its operationlets (Arrowhead Ripper in particular) that top level Al-Qaida leaders have escaped the trap. In fact, The Fourth Rail puts it about 80% of the high level Al-Qaida leadership has left Baqubah.
A couple of things. The force attacking AQ in Baquba is a corps directed force. That, sports fans, is a large number of people. You do not move around that number of men and equipment in an urban (or practically any) environment without notice. In fact, Bill Roggio passes on reports that
So the bad guys had plenty of time to leave. If Tony Soprano knew the cops were going to be driving to a place he was going to meet someone the next day to bust him, think he would keep the appointment? Do not underestimate the elimination of middle and lower management. Who becomes upper management after the US Military retires upper level AQ management? There is a lot of institutional memory and skill being wiped out.
In any event, Team AQ just lost its Iraqi capital and is moving it, do you honestly believe that to be a good thing for Team AQ? Ask Jefferson Davis about the fall of Richmond.