I take you to George Wallace standing on the steps of University of Alabama with JFK ordering the Alabama National Guard to escort a black student therein per a Federal court ruling. Despite the fact that the governor of each State's guard is its supreme commander, the Guard obeyed the President as commander in chief.
Rush is correct in every respect except for who controls the guns.
Actually, even w/r/t the power of waging war, the People have the right of Mutiny. Elaine Scarry (who was really writing about something else, viz. nuclear-weapons doctrine and the 2nd Amendment) pointed out in her 1981 opus magnum, so to speak, that she wrote while at U. Penn., that the Framers reserved, when they wrote the Constitution, three distinct loci of power for the People and the People only, to keep them from being bullied and abused by their government(s), the federal government most expressly because it was the federal Constitution at hand.
The three area of power reserved to Us the People are the ballot box, the jury box, and the cartridge box. The People have an unreviewable right to elect whom they please. The People have an unreviewable right of jury nullification. And lastly, the People have an unreviewable right to Mutiny, to refuse to fall in for Acts of War they find repugnant, to refuse orders they find odious, and to resist tyranny with the arms they have a right to bear in their own defense.
She made these arguments at doctoral-dissertation length, but that's the short version.
Military authorities have frowned on a right of Mutiny for obvious reasons, but Scarry argued powerfully that that right is there. If an entire State's Militia refused presidential orders, as in 1861, the military authorities would play hell trying to make charges under UCMJ stand against the whole State in arms. In 1865, they didn't even try.