My guess is that the US was doing Pakistan a favor - I suspect that the Pakistani government is afraid of the popular reaction if it was seen as the one killing Mehsud. They know perfectly well that everyone already hates the US in that part of the country, so it's not like this will make our image worse in the pro-Taliban areas. Now the government can just lodge a mild protest about US action and privately celebrate his death. It could be that the Pakistani president and army chiefs were worried that the ISI or rogue elements in the army might even sabotage the operation, so they had to quietly get the Americans to do it.