If some rogue element (americans) tried to shoot down a plane carrying a witness to a conspiracy to overthrow a legitimately elected President, they could/should be prosecuted in a military tribunal?
I don’t see why not, if the conspiracy to overthrow is part of a covert war. They would be unlawful combatants. If they caught them at it, there is no need to bring them in IAW LOAC.
An unlawful combatant is acting on behalf of an enemy of the US. It could be applied domestically in time of civil war, but otherwise it would normally be a foreign enemy. If the rogue American was acting on behalf of radical islam, with which we are at war, you could make the argument that the American is an unlawful combatant and try them before a Military Tribunal. Under the SC decision that we talked about a while ago, the rogue would be entitled to a hearing as to whether they were an unlawful combatant. That could also be a military proceeding or a civilian one, so long as due process were observed.
If the rogue American is acting on behalf of a band of CIA deep staters who want to control the US government, that would be treason and attempted murder, but perhaps not allow for a military tribunal.