I absolutely would bet on it. There may be a few who would “just follow orders” but I would bet that the great majority of the military would be on our side.
The orders of the Commander-in-Chief will go down through the ranks from the highest generals to the NCO's in the field. If they are ordered to fire at patriotic Americans, their orders will inform them that these people are "insurgents" and "traitors". Those orders will be followed, and anybody who does not follow those orders will be shot on the spot.
But it probably won't come to that. When the drones and biological weapons are deployed under martial law, FEMA will be able to handle it. Federal paramilitaries will simply follow their orders because they always follow the orders of those who pay them.