Musharraf is alive as long as he does not act very strongly against the Taliban. Taliban is a creature which ISI has created with the specific purpose of increasing Pakistan's influence in Afghanistan. 911 created a situation where Pakistan could not support Taliban openly but with war in Iraq going wrong, ISI has got emboldened and is back to playing its old games. I doubt if Musharraf has any control over the rogue elements of ISI.
However - he has nearly a year to sort this out because US would withdraw a large % of troops from Iraq and redeploy them in Afghanistan. My feeling is Musharraf will cave-in and tacitly allow US a free hand in North-west pakistan as in any case he does not control that territory. He may want US to fight the dirty war with ISI and Taliban on his behalf. His cleverness on this account will lead to upheaval in the next 3-4 years. The westernised elites in Pakistan will support him but masses will turn strongly against him