Looking at it, it seems like Ions are stopped by FFs? If that's the case, then removing the mark restrictions might be okay, since you could protect your expensive stuff from the Ion blasts. The problem being that the only ship that can reliably make a shield big enough to cover a lot of ships is a Champion, which some people might not be playing with. Riots would be okay, but they can't cover a lot. In any case, removing the level restrictions still strikes me as inelegant.
One idea that popped into my head and of which I have not really considered the implications is to make the Ions do AOE damage in addition to insta-killing ships lower than their level. So, if a blob takes on a Mk. II Ion cannon, it would target the Mk. II ships. They'd insta-die, but the impact would also create an explosion capable of damaging nearby higher-mark ships, similar to how Area mines still damage mine-immune ships if a regular one triggers them. It makes an Ion cannon a decent threat to a mixed fleet without guaranteeing expensive losses, as well as being useful for the players.