It's easy to see why Al Qaeda might prefer McCain, and preferred Bush. The longer the USA can be engaged in fighting in Iraq the better from their point of view. There's no reason to think Al Qaeda is particularly concerned about the effect of that conflict on Iraqis, they are merely pawns in a longer and wider game, in which a key object is to paint the USA and its allies into a corner as enemies of Islam. It is easy to see why McCain, like Bush might be seen as a more reliable partner in achieving this gaol of continuing and extended conflict.
However nothing can be taken as to face value. Obama's talk about Pakistan might also appeal to Al Qaeda strategists hoping for a wider war - and issuing a press release backing McCain might be seen as a way of discouraging people from voting Republican.