We used to have a system like this. I thought it worked pretty well. Sure it wasn't perfect, but I liked the transparency.
Nothing I'm saying is defending the actions of the citizens in question, only criticizing the propriety of the executive branch unilaterally killing a US citizen without due process outside of situations like your hypothetical where dangerous direct physical violence against American forces is involved. If the government had instead forcibly arrested them and kept them in custody while putting them through the criminal justice system, I'd have no criticism, assuming they had adequate evidence. I'd also want them to release the accused in the unlikely event of an acquittal (since government accusations can be wrong), but the regular courts are very good at convicting people who actually do stuff like this and federal prosecutors are very good at their role.
One helpful analogy is to imagine what would happen if we entirely removed the foreign flavor, since after all we're discussing the attempted killing of a US citizen by the US government. Suppose instead that the US military had strong evidence that entirely domestic groups, unlinked to any global extremist Islamist movements, were doing communications or logistics in support of a planned attack a domestic US military base. Maybe this hypothetical attack is due to dissatisfaction with, or skepticism of the legitimacy of, the government in power.
My guess as to what would happen in that scenario: law enforcement would be directed to arrest the people involved and hold them without bail for criminal trial, and would be authorized to use whatever force is necessary if there is physical resistance, including lethal force if necessary. The goal would just be to arrest, however, with killing simply accepted as a possible accidental result.
Something similar would likely have been appropriate here, albeit with the involvement of the military due to the location outside the US and the high likelihood of violent resistance.