There is little doubt about the devious intentions and actions of these two individuals. While both held U.S. citizenship, they railed against the U.S. government and called on Muslims around the world to kill innocent Americans with the same viciousness as the late Osama bin Laden, Awlaki through his sermons and Khan through his magazine. But it's still unclear whether the two men ever actually took part in the direct operational planning of any terrorist attack. This, combined with the fact of their U.S. citizenship, has already begun to spark debate in the U.S. and other civilized countries about the legality of these assassinations, if not their necessity. Keep in mind there should be, and has been, a clear line between inspiring violent action and carrying out violent action.
The outright condemnation of these assassinations is difficult given that media reports have indirectly linked Awlaki to at least two terrorist operations; the Christmas-day underwear bomber and the attempted mailing of explosives to the U.S. through freight airlines - however there's less evidence for Khan. Additionally, without access to classified materials on the two men the case for reproach is made even more challenging. All of that being said, Awlaki nor Khan were ever charged with a crime by any U.S. court prior to their assassinations. So make no mistake, this was indeed an extrajudicial killing of two American citizens presumably by the U.S. government.
However, terror, murder, assassinations, and extrajudicial killings have been a part of war for some time and will likely continue. Therefore the question arises, as a nation that values the rule of law and the order that comes with it, where will the U.S. draw the line for future operations, if at all?