I agree that whether the targeted killing was moral and whether it was legal are two different issues. However, it's incorrect to say that the claim that the killing is illegal is a "fact". It's a legally defensible position, but it is not a fact. It's a position asserted by the ACLU, but rejected by a federal judge:
Anwar al-Awlaki - Wikipedia, the free encyclopedia.
The judge held that the program was a legitimate use of executive power, and thus judicially unreviewable.
There have been executive orders restricting assassination, but it's not clear that they apply here (and the courts don't seem able to enforce them). The Bush administration for example argued that targeted killings were always legal during a time of war, and that we have been in a time of war for the last decade.
The sixth amendment doesn't apply. It refers to rights during criminal prosecutions. It doesn't guarantee a criminal prosecution. A firmer foundation would seem to lie in the Fifth Amendment's promise of "due process". Indeed, the Wikipedia article on the Fifth Amendment currently cites three sources debating whether it ought to have prevented the killing:
Fifth Amendment to the United States Constitution - Wikipedia, the free encyclopedia.
I'm quite sympathetic to the claim that such a killing is illegal or unconstitutional, but it simply is not a "fact".