I like the idea, and it would be a great addition if the abuse problem can be solved.
I think the Guard ID requirement is definitely a step in the right direction. My suggestion would be to have an extra piece of equipment, similar to an ID, that you could mount to you ship, and only having that equipment would allow you to use the command. Then you could put limitations on that equipment, maybe make it not sold at bases, and only given out by faction leaders and special requests to admins. That way, it severely restricts the number of people that could get access to it, and demands a certain level of responsibility and accountability. If a player abuses it, pull the item from him. If a faction abuses it, pull all of the items from the faction and the leader.
And yes, this would be most useful for locking bases and trade lanes.