You asked him, not me, but I think it goes way beyond that:
(1) I'm betting Musharref knew about the nuke sales. Why do you think Khan has been pardoned and allowed to keep his loot? So he'll have a good reason not to say, as a friend of his reported he told him, that his superiors knew about his activities.
(2) No way did Musharref voluntarily initiate the prosecution of Khan, a "national hero." There's another thread somewhere about how the U.S. came to him with clear proof and demanded action. We're keeping this low-key so as to give Musharref a plausible lie about it being an entirely internal matter, but this was a U.S. operation all the way.
(3) No way would Pakistan have acted unless they were terrified that the U.S. might take them out if they didn't. I'm betting that after 9/11, and a good look at the strategic map, we went to them and said: you want to be a friend regime, or an enemy regime? Afghanistan and Iraq gave them a good look at the fate of an enemy regime.
Now, try to imagine how much of this would have happened if Gore had been President. Or Kerry. This alone is enough to give Bush my vote.