That is what the stress and Ion tokens are for. No actions and a ramp up speed wise. Agility doesn't represent acceleration in all ships, and having a penalty like that would unfairly benefit the slower ships. A stress and ion token affect all ships equally.
Except that ships aren't that vulnerable when they're ionized. Additionally, I think it would be hard to justify the effect, and you'd have to deal with upcoming abilities that deal damage to ionized targets (I'm thinking Dace Bonearm here). A similar issue follows with assigning stress tokens, where it's hard to justify the effect, and certain pilots can game the effect.