I'd be more concerned about all those service members who have had it drilled into them that they should not follow an illegal order.
And now anything the CoC says is legal, is.
Oh, and the new ruling specifically bars prosecutors from inquiring as to the POTUS' motives - so you couldn't ask the Joint Chiefs, for instance, what he said before he had troops open fire on protestors on the Mall. Just that it was official. And legal as a result.