I think you're right. Very interesting situation. I suppose our agreement with Pakistan could change if we determined that Muscharraf was not in control. Pakistani supported terrorism might be all the evidence needed to change that agreement.
But we need both Pakistan and India working with us, so I don't think we'd dump either unless there was absolutly no other choice.
Actually, I don't know if I was right or not. I came across this while I was looking for something else in my notes.
http://www.freerepublic.com/focus/news/650610/posts China, Pakistan sign secret pacts: Military agreements raise concerns over nuke technology