If you really want to come up with a super weapon to use against the Vong, think logically. If they use biological equipment, what are they most vulnerable to? A Virus. Come up with some horrible thing that kills them off. (Return of the Krytos virus maybe? They could take Coruscant and when they're reducing the planet's cities to rubble they expose some hidden water reserve that hadn't been purified of the virus...) Just an idea...
The thing about the Ion cannons is that it's too easy. Think of all the battles the New Republic and even the Empire have fought against the Vong. Surely SOMEONE must've fired they're Ion cannons before. At Ithor maybe? When ALL those ships were there?
Just my two cents...
Rogue 9's words of wisdom