In a word, no. That EO, and the whole series it's part of, don't restrict the DOD. They restrict the intelligence community. Nothing stops the military from targeting a head of state - or literally anyone else - if they are declared a legal target / combatant. Not sure where this whole "the military can't kill certain people" idea has come from. Probably news organizations like CNN, NBC, ABC, et al who just clip one-liners from EOs and use them to promote narratives which support their own motives.