One of the many nice things about 'Sector is that many limits are soft limits, meaning that you can exceed them, but at a price. The limit on command points is unfortunately exempt from this, which can lead to painful situations where you have to watch ships fly into a certain death that one right command would have avoided.
IIRC Alex has once said that CPs represent the player character’s ability to communicate with his captains during battle, and that too much communication would disrupt the ability of a captain to effectively command his ship. I think the CR system gives the game the ability to simulate this disruption, instead of leaving it to the players imagination why he can’t issue any more orders.
When at 0 CP, keep the ability to give commands, but instantly reduce the CR of any ship that gets a direct command/takes up a newly created assignment. (I suppose ships that take the assignment subsequently should not get their CR reduced.) Of course it would have to be clearly communicated n the UI that you pay in CR now.
I think with this the point of CP, which is to reduce micromanagement, would be preserved, but without the sometimes dire and frustrating consequences.