Ion cannons disappear to enemy fire when they aren't covered with a forcefield, and they're highly prioritized; as well, a destroyed enemy ship per four seconds on the player side is nothing because in opposed to the player in having to waltz around an AI planet to destroy guard posts, ships and such, the AI essentially goes for harvesters and the command station, leaving less time for attrition.
Again, a counterwave that is multiplied by the penalty means no planet is safe, and may mean a game over anyways. Ever had a wave of a thousand cloaked ships in your inner worlds with your military far from range? Those stealth ships will spread out and create unimaginable pain after destroying the ion cannon in one second.
If the penalty can't be removed, I would suggest that ion cannons be simply a non-captureable. It's silly of them to be an immediate gratification from "salvage this for X resources, congratulations." Additionally, new players which are unaware of the penalty are going to be suffering from this, as usual.