It's some revolting level of corporate scheming.

All the other companies in the MS Alliance decided to exclude the Gund-Arms because they want a monopoly. Nothing more. The ex-military guy is using the risks that going high PMET score can cause as an excuse to outright exterminate them, to a degree that the president of the MS Alliance was kind of shocked at how brutal Cathedral went with all this.

My understanding is that it isn't an EMP wave, though it works like one. It's specifically disrupting the link technology the gundams use. It should similarly kill or at the least paralyze cyborgs using the same technology, but Ericht's mom only has an arm(?) and she wasn't using it anyway so she could share her space suit's air with Ericht.

So the "EMP" disruptors are probably insanely expensive and can't be mass produced. They were on a bespoke model. I expect them to be dredged up later out of mothballs, because Cathedral assumed a decade later that the last suit and their pilot died in the void.