I think drawing is a bad idea, but adding a toolbox of different markers that the commander can put on the minimap (with strict limits) would be great.
Why limit it. If the comm is going to grief they will just research mediums or drive the CV into the water. If a decent comm is just drawing YOU SUCK 8==D all over the minimap, then the team probly wasn't listening does suck.
I agree with you but I think adding waypoints to the move here command and having the toolbox of markers would be the best chose. Also I think that the small mini-map should only show the orders he or his squad was given, but if they enlarge the map ("M" or "Enter") he will see all the orders and markers given by the commander to everybody on the team.