Following the Chain of Command, the CE commands the ship and outranks lieutenants, if a SO refuses to follow his orders and continue to disrupt briefing, he is to be arrested.
According to the Marine Law, Jones have the same rights of a marine, if he is harmed by someone, that person is making a crime the same way of harming a regular marine.
About the last question, I am more old fashioned in military culture, the Sabre could do the job perfectly, the Synth could have the baton