depends where they are.
You get 1 merit for killing an enemy commander at your expansions, if you are in a combat power, not sure about the delivery powers.
You also get 1 merit for killing an enemy commander who is in one of your control systems, and you get 1 merit if you kill an enemy player who is in their control system.
Good point, though I think if they looked at how very slow that process would be compared to the currently-popular style of undermining, the fear of exploitation might pass.