No, complete sense. If one is being given orders by the Government, by definition they can't be defending the populace against that government. Again, that's the whole idea behind the Bill of Rights.
The organized portion of the militia IS the portion run by the Government. They're the ones who are largely responsible for defending this nation against foreign invaders, or terrorists, who whoever.
That's NOT the militia being referred to int ehd 2nd amendment however, as I've already explained. The militia in the 2nd amendment can't be run by the Government.........unless you're saying these government employees have changed sides (in the event of an overt oppressive regime attempting to take root) In that case, they're no longer taking their orders from the Government, so local folks, such as sherriffs and the sort can definately be considered part of that 2nd amendment militia