It can have an effect against non-rulebreakers also. If your opponent in a Gunboat cruises away, lets say for examples' sake you don't or can't CD them for some reason, and pursue with cruise engines. You've already spent your energy, which is not recharging at this point.
Now for the sake of example, lets say a fighter comes along and disrupts the escaping Gunboats' cruise engines, the Gunboat immediately starts to hammer on you as you approach, and while he still has full energy , you find yourself unable to fight back until your energy recharges.
It may also have problems the other way around, if you yourself are fleeing on cruise in a capital ship and are intercepted and unable to defend yourself because you have no energy left.
But my point is that this won't stop people from cruising to catch up. It will give them a slight disadvantage, yes, but whats' to stop them cruising, engine killing once they reach max speed and letting their energy refill before they get back into range? Its' the same concept as thruster drain. The rule will still need to exist, and the rule presently exists and works fine.