Updated Below (I and II)
In a recent Asia Times article Saleem Shahzad compared the current policy of the US towards Pakistan to the actions taken by the US against Laos and Cambodia in 1969. Then with the situation worsening in Vietnam Nixon turned to bombing campaigns against North Vietnamese sanctuaries in Laos and Cambodia leading to disastrous consequences for the region and its peoples. Now with the situation worsening in Afghanistan the US is again lashing out with possible dire consequences for the region and its people. Shahzad's pieces tend to hyperbole but the way things are going maybe he isn't too far off.
It is not entirely clear who is in charge of US policy towards Pakistan. During the summer it seemed that the US supported the idea of Musharraf serving out his term albeit with little or no power. Zalmay Khalilzad had other ideas and with the classical neocon predilection for making a bad situation worse he provided Zardari with the backing to make a successful bid for the presidency. In Zardari we have a leader totally beholden to the US. This is not a good thing. While we can be certain he will accommodate us to the fullest extent possible what we actually need in that part of the world is an ally with some local credibility - not a paid goon. And Zardari in Tariq Ali's words "is the worst possible slice of Pakistan's crumbly nationhood." With a popularity rating of 14%, despised by his own party activists, he is not someone who will be useful in winning hearts and minds for the US in Pakistan.
The conflict we are now facing with the Pakistani army is one of the unintended consequences of Zalmay's grand adventure. The military has been unhappy for some time with the role it has been assigned by the US. There have been mutterings of US perfidy and rumors, especially in military circles, that the US is playing the jihadi card against Pakistan and secretly backing Beitullah Mehsud and the Pakistani Taliban. There is a Turkish saying that the thief fears for his house and the pimp for his woman. So this is probably a case of worrying about being done by as you did. While the US has done some stupid things in that region backing our own jihadi forces against the Pakistanis would be beyond moronic. However, the fact that such rumors are being spread and believed by people who should know better shows the depth of suspicion engendered by the US. The recent US incursions into Pakistan provided an opportunity for the senior officers in the military to show their displeasure with the policy being pursued by the government. Musharraf could probably have contained it. Zardari cannot. And Kayani is too new to command the kind of loyalty from the corp commanders that Musharraf did. What we are witnessing is pretty close to a revolt within the army against the Chief of Army Staff. This is an extremely dangerous situation. Unfortunately, all indications are that things will only get worse. US policy towards Pakistan is no longer being managed by the State department. All indications are that without effective civilian leadership the US military is making policy. With all due respect to the US military, militaries by their very nature focus on the short term sometimes to the detriment of the long term. As for the presidential candidates I leave you with Tariq Ali's recommendation to Obama (h/t A Tiny Revolution)
It seems Kayani is doing some housecleaning. (h/t Cernig) I don't know how effective that will be in the long term if the current US policy continues.
There are unconfirmed reports that Beitullah Meshud has died apparently of natural causes. If true this gives the Pakistan Army some breathing space. On the other hand it might just be a ruse to relieve some of the pressure being felt by the Pakistani Taliban.