I think you misunderstand me: I’m not questioning his involvement in al-Qaeda. But the fact remains that he was a US Citizen. Being a citizen typically entitles people to certain perks, like due process in a court of law. This was denied to him, which is why the ACLU took up the case. The state has the power to execute someone, but up until this precedent was set, it was only able to legally do so after they had been convicted in a court of law. Intelligence agencies do not fall under that umbrella.
The country he was seeking refuge in had even ordered him to be captured dead or alive.
This is entirely irrelevant to US law. If, say, I was in Bolivia, and the Bolivian government had an active dead or alive warrant on some US expat, it would still be a capital crime for me to kill that man on Bolivia’s behalf.