Since the Pakistani people apparently believe it was the ISI, army or Musharraf, it makes an al-Quaeda move look more intellegent if they did it.
If one were to look at this from al Qaeda’s point of view, it would make perfect sense: first, you kill an opposition leader; then, you spread rumors that the current president did it; after that, you mix some gunmen in with the protesters and shoot at the police/troops to get them to fire back and kill some innocent by-standers; at which point, things WILL get out of control and you can make some more gains in the chaos.