I was actually having similar problems with the ElectroMag weapons in the B5 Mod, I wound up making some Shield Only, some Engine Only and some mess the ROF delay.
I like SJ's idea about the "Only Security Stations", though it might be better to make it the "Only Engines" (since one of the things the Ion cannons did was disable the ship without damage) and add that to components that should be effected - thereby translated "Only Engines" to "Only ElectoMag/Ion". This way you can add the ion effect to the game without taking away from the boarding parties
