I'd go with the higher too, reason being the vessel/craft has only one offensive EW system operating. (In theory you could have multiple systems but I have a problem with them being all on at once, they could interfere with each other, harmonic frequencies, effect owning crafts sensors etc.) Having multiple operators "playing" with it at the same time is a good way to mess it up.
Evil thought, don't tell players this let them all have a go and then roll for an increased fumble or even breakage on the system. Two operators double fumble range, three triple. Still only take account of the highest skilled characters roll for how effective the system worked, assuming they didn't break it!