Most policymakers and pundits don't seem to know how to deal with Pakistan. (I certainly don't.) On the one hand, the United States wants Musharraf to be more aggressive about hunting down Al Qaeda operatives in North Waziristan. On the other hand, moving too aggressively against that part of the country might cause Musharraf's government to collapse, in which case radical Islamists could seize power--and with it, control of Pakistan's nuclear arsenal. Bad news all around.
At any rate, I'm curious to know what sort of safeguards Pakistan has in place to prevent its nukes from falling in the wrong hands, should, say, Taliban sympathizers in the ISI stage a coup (or whatever). The reporting on this front seems patchy. In 2004, Graham Allison warned that the security measures were still much too flimsy, and wanted the United States and China to do a thorough review of Pakistan's nuclear stockpile, in order to help Musharraf set up proper controls. That would involve a lot of delicate diplomacy--especially since Pakistan is understandably reluctant to open its arsenal up to outside inspection--but it doesn't seem completely undoable.
So what's actually being done? A Congressional Research Service report in 2005 noted that the United States was offering some assistance, but mostly to "focus on helping secure nuclear materials and providing employment for personnel, rather than on security of nuclear weapons." See also here. And last August, Pakistan declared that it had set up a "tri-command nuclear force," but it's not clear whether that would safeguard the weapons in the event of a coup. (In any case, the country's past assurances on this score have been fairly suspect.) Those seem to be the main media stories of late. Who knows, perhaps the administration really is doing all it can here, but I'd sort of like to see a closer investigation.