What if ion tokens could exhaust an opponent's upgrade card for a turn? It would have to be a part of the ship itself, not an EPT. And you can't really ionize a hull upgrade, so I think it couldn't really affect modifications.
But what about system, tech, and secondary weapons? No, you can't fire that TLT this turn because I ionized it. No, your Fire Control System does not trigger to give you a Target Lock.
Too strong? Then make it require two or three ion tokens.
It should be an either/or - you can't make your opponent space drift AND exhaust one of their cards as well.