Such would only be justified if there was no way, within the system, to achieve the desired goals. If I understand the decision, it really just requires that Congress make explicit what the expectations are. Congress has the power to declare war, not the President. Congress has the power to legislate the structure of the lower courts, not the President.
The failure of Congress to act is to be addressed by holding periodic elections. Not by granting the powers of Congress to the President.
Politically, this is a great decision. If the Demoncrats want to interfere it will be timely for the upcoming election. Let's see the anti-war Demoncrats expound on why we should not hold these terrorists accountable.
"Congress has the power to declare war, not the President."
But once the Congress has granted the President the authority to take military action, which I believe did, after 9-11, HOW he does so should be HIS call, not Congres' or the Courts.
Nevertheless, your point about forcing the Democrat pacifists into a corner is an intersting one and I hope it plays out as you and I hope.