You mean the Marines could walk into the state department, come up behind a secret member of the muslim brotherhood working at one of the desks, stick his service Beretta behind his ear and pull the trigger, and it would be perfectly legal?
One of the 'protections of civilian status' is they can't be killed intentionally. Collateral damage: Collateral damage is any death, injury, or other damage inflicted that is an unintended result of military operations.
Obviously civilians are killed in war in a non-criminal way 'unintentionally' or a criminal one 'intentionally'. Civilians who forfeit the protections afforded civilian status by engaging in hostilities can be killed intentionally.
In your example, a 'secret' MB member would still have civilian status until his actions exposed him as participating in hostilities. So no, you couldn't do that in that example. Put the still 'secret' MB member in another venue where he has exposed himself as engaging in hostilities and yes he could and probably would be killed even though ostensibly a civilian, just like an identifiable enemy soldier would be.
For the purposes of further, if the US 'knows' via intel sources that a foreign national not legally recognizable as a 'combatant' (uniform, chain if command, state sponsorship) is engaged in hostilities against the US, IMO there is no legal bar from killing him by lawful means. Like Osama BL, these folks have placed themselves 'outside' of Geneva Conventions protections, and while there are some nations that would object, they are the same ones that seek to prevent the US (and other capable countries) from exercising that ability. IOW asymetrical war for me not thee.
In post 371 there is a link to a challenge to a section of the NDAA of 2011, signed by the Bummer, relating to the use of military tribunals for USCs. 0 claimed he would never use that section, probably because he put it there for Hitlery. But she lost, it is still in force. Was suspended by a US District court, the suspension overturned by the 2nd Us Court of Appeals (then liberal) SCOTUS declined to hear it. Still operative AFAIK, a tangled web for sure.