“What about when you’re an enemy combatant?”
As we saw with Jose Padilla, if they are on US soil, they still have the full protection of the US legal system, like habeas corpus, right to counsel, right to trial by jury, etc. Hence the later use of renditions and foreign detentions to try and avoid all of those hassles.
Jose Padilla didn’t conspire to assassinate a US president.
I don’t think we’ve seen the limits of what can be done about this sort of thing. Or the limits of force in the will of the American people.