So what will happen with US-Pakistani relations from here and what will be the longer term effects?
(Asking if they will “survive” seems silly, no offense. There will be relations. The question is what sort of relations and how those changes in relations increase or decrease our security and our other interests.)
So if Pakistan did not have nuclear weapons you think the US would still consider them an ally?
From everything I have read about Pakistan their government is as corrupt as it is incompetent. That said, they are a soverign nation and they can do as they please. They have enough valuable resources and strategic location that they are important to US interests so we will be mutual allies for a long time to come.
I read an article awhile back (The Economist???) about just such a possibility if a coup by radical islamists succeeded. Apparently there is an agreement for US forces to secure Pakistans nuclear weapons if such a scenario occurs.