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The issue, if there is one, with Obama's comment is not that he was discussing with the American people our foreign policy. It's that he was discussing with the Pakistani people our foreign policy.
Bush was rightly excoriated for saying openly that, if China attacked Taiwan, we would defend them. It was not foolish to say this "on its merits"--most people here would agree that defending Taiwan would be both a moral and strategic imperative--but because it emboldens pro-independence forces in Taiwan, and creates a face-saving problem for the Chinese government, which they generally respond to with bombast and threats. It costs us money and international reputation.
Obama's comments, aguably, create a similar issue by giving Pakistani "Islamists" a stick to beat Musharraf with; and while Musharraf is no great friend or ally, we need to ask ourselves: who will rule if he falls? How does it benefit us to weaken his standing?
The principle at issue here is strategic ambiguity, and all nations use it as an important foreign policy tool (e.g., China's ambiguous assertion of sovereignty in the South China Sea). I'm also not sure I agree with your assertion of "secrecy" on the part of the foreign policy community; you can find a lot of frank discussion of the very issues you speak of in, say, Foreign Affairs. It doesn't really matter, from a policy perspective, if you or I or some other gadfly or even a Serious Foreign Policy Analystâ„¢ says that we should attack Al Qaeda targets in Afghanistan with or without the approval of the sovereign ruler of that country. If and when Barak Obama becomes president, however, is previous unambiguous statements on the subject will, without doubt, have substantial foreign policy implications, not only for the U.S., but for Pakistan as well.
The only thing left to argue about, really, is whether this is a good thing or a bad thing. By making such a statement, Obama has failed to walk softly; however, this could even work to his advantage, as long as he carries a big stick.