Players can deliberately trash the efficiency of captured worlds by redesignating them multiple times until they are so inefficient that they are unable to do anything, or by removing organic food/survival goods in transports until almost everybody on the planet is dead.
There should either be a cooldown that limits how ofter you can redesignate a world, or a couple minutes grace period after redesignating a world where you can redesignate it again with no penalty. It should also be impossible to remove any resources in transports during a civil war. ("Dockworkers refuse to load transports because of rebel threats" or something like that.)
I'm not opposed to having some sort of "raze" function that loots a planet, destroys structures and immediately sets it independent.
Some ideas:
1. Make redesignations and/or removal of critical supplies impossible for a relatively long period (or only possible with a large occupation force and efficiency loss). We can refer to it as the imperial integration time.
2. The previous owner can retake the system and return it to its previous state with minimal/no efficiency loss during the imperial integration time.
3. Make a raze planet command that will devastate the planet over time. This option should cause massive imperial unrest (unless in retaliation for the same?).
Maybe starcruisers coild perform orbital bombardment of hostile planets to kill population, reduce efficiency, and destroy structures without actually invading.