Washington as a sitting President rode at the head of an army to suppress the Whiskey Rebellion in Pennsylvania. Consisting of mostly militia raised to stop riots and rabble rousing in related to liquor taxes in the back country.

While the motivation level of the individual soldiers varied the force was very much prepared and ready to use force to restore order. And it was just an evolution of events that the movement collapsed before their arrival.

So yes even divorced from the Continentals, Washington was prepared as President to use force as part of his powers with resultant deaths.