Anybody affiliated with an Al Qaeda franchisee is covered by the Congressional AUMF, which has not been rescinded, to the best of my knowledge.
You know I get what you're saying and that I generally agree with it, but per your earlier "Not without an official declaration/authorization by Congress, which would not make them extrajudicial" statement, there's a Congressional authorization in effect with Al Qaeda members.
(And I believe your reaction is generally the right one. Any American who mindlessly high-fives his buddy when the Executive branch uses flying killer robots to snuff out a US citizen just because he was told the guy was a baddie worries me. To paraphrase TGS, I don't just want to see the receipt, I want to look at as much of the books as pragmatically possible.)