I decided to investigate other player's report on misbehaving /gc fleet stop and tried to see how it works myself.
Just tested this on my B.O.B. while sitting in its cockpit. /gc fleet stop turned on inertial dampeners but did not turn on thrusters, which, of course, did not effectively stop the ship.
I'd suggest turning on thrusters and disabling all overrides (same with gyroscopes), like I do in my "Emergency Stop" script here: http://steamcommunity.com/sharedfiles/filedetails/?id=515022499