Andrew McCarthy has responded to Kevin Williamson’s argument against President Obama’s approval of assassinating al Qaeda figure and American citizen Anwar al-Awlaki, which I mentioned here. As he typically does, McCarthy makes a strong argument, but I think the sides in the dispute might be circling around the ground that might lead to accord.
One point that McCarthy makes is that the President is constrained by political balances:

Could a president abuse his powers? Of course. All power can be abused — including legislative and judicial power. But the basic check against that possibility is political, not legal. Mr. Williamson implausibly argues that “political limits” are inadequate against the president and must be supplemented by “legal limits.” Courts, however, have no power to enforce their injunctions — for that, they must rely on the executive branch, and an executive branch that maintains a list of citizens it plans to assassinate will be unlikely to enforce injunctions against itself. By contrast, a president who really did the horrific things Mr. Williamson imagines President Obama doing would find his war authorization rescinded, his military and intelligence services defunded, and himself impeached. A president guilty of less heinous excesses might not be impeached, but he would find his popular support dramatically eroded. As Mr. Obama is finding, that has political consequences — among them electoral ones — that curtail the presidential capacity for malfeasance. This is the genius of the system.

Put aside the question of how explicitly and repeatedly a president would have to assassinate American citizens before the picture had become sufficiently clear for Congress to defund an entire military operation. McCarthy elides, in this paragraph, the relevant point: The degree to which American citizens insist that the executive branch treat assassination (especially of citizens) as a special case — requiring judicial oversight and Congressional input — factors into the political calculation that the President makes. That is, if a judge declines to bless a particular assassination order, the President may not have to listen, ultimately, but the political cost of doing so would add an exponent to the backlash against the order in the first place.
Politics also play in a tangential point of McCarthy’s:

That’s all the assassination authorization for Awlaki is: legal cover if circumstances arise under which killing him is the best military option. And here we arrive at the central absurdity in Mr. Williamson’s argument. Though minimizing him, Mr. Williamson concedes Awlaki is a bad actor and has no objection to his being killed on the battlefield. Since Mr. Williamson doesn’t see that as problematic, he can’t fathom why our armed forces would want insurance — though it is they, not he, who would be hauled into court by Awlaki’s family. But the authorization to assassinate Awlaki does not mean the administration would have him killed if it encountered him coming off a plane in Chicago, à la José Padilla — a U.S. citizen captured, not killed, by the Bush administration. Nor does it mean our forces would kill Awlaki if they could apprehend him in a foreign country under circumstances in which detention was the more practical option, à la U.S. citizen Yaser Hamdi and al-Qaeda bigwig Khalid Sheikh Mohammed.

As I’ve already suggested, assassinating U.S. citizens ought to be such a sticky matter that those who undertake it should have to think it so important as to risk legal repercussions. If a particular target justifies the decision’s being made at the highest levels, then let the President seek the cover of Congressional or judicial approval.
Ultimately, the Williamson-McCarthy dispute comes down to what process must be followed to determine that an assassination is legitimate. One side believes there must be maximum oversight, and perhaps understanding that the process of gaining specific oversight would make the result politically untenable, the other side is content with the general oversight of politics writ large.