Inactive Militia are under no such stricture. So the active duty militia is "bound" to the civil authority. The inactive isn't. Therein lies a stumbling block for more than one persons arguments.
Of course, the protection is broad and general and applies to all US Citizens not subject to a criminal penalty. Regardless of the "home rule" status claimed by their city/State.
yep - see recent USC citation at #150
funny how almost no one (except the hardcore 2Am folks) refers to the actual legal definition of Militia in these arguments