I can see the good and bad sides of such a system.
YAY:
It stops people making themselves neutral to you so they can shoot you
Stops people who shouldnt dock on your base from doing so.
Gives a tactical advantage to people being in your system.
NAY:
Exploitable as shown previously
May have problems when multiple allied factions are involved as mentioned previously
Overall:
If the exploitability is taken out of it i would be a happy to use this command in battle.