That makes no sense. Both parties are under the same exact mechanics. If the cruising player is running, his energy is screwed the same as yours, hence it is equal. If you're cruising and have to stop to attack, the attacker's energy is doing the same thing as yours.
Either side is facing the same mechanic. This would be implemented to hinder a capital ship cruising after a thrusting player. It may not kill the issue in one fell swoop, but it's something.