I'd be happy if Pakistan's Musharraf helped us in rooting out al Qaeda. But, I'd be just as happy if we told him, in the kindest terms, "Pardon us, but we're going to come in and do a little housecleaning. Hope you don't mind."
As this New York Times story contends, one of the reason 9/11 happened is because we didn't invade Afghanistan and destroy al Qaeda beforehand. I suggest that we don't make the same mistake twice.
If the Pakistanis don't like it, then I suppose it's something we'll have to live with. But certainly, Musharraf needs us just as much as, if not more than, we need him.