I've found that bringing Vader and Boba helps, because they don't get targeted by the Ion. (not sure if they are immune) The same goes for magna cannon. Bring in the falcon and Katarn. The hero ships are powerfull enough to turn the tide. Also, the Accuser's special attack still functions, if you can get it close enough before it's disabled. When I know there's Ion cannons, I don't even bring ISD's, as they take up too many pop cap points when disabled. One last thing, capture the space build pads if there are any, and build missile launchers to attack station hardpoints. They are immune to the Ion.
Gary Swift (aka gswift)
Lenexa, Kansas USA
You can try to monkey-proof your program, but you'll never monkey-proof the monkey.