instead of deactivating augmentations they cause them to malfunction, rendering the person with them largely useless for anything, which makes using it as a control device worthless. It's also inconsistent with the first game, where a kill switch literally exploded someone, so the threat of it being triggered functioned as the control mechanism which kept them in line.
So this is a different type of kill switch obviously, one which is designed to keep the general populace in line so maybe causing their heads to pop is a bad idea. Don't you think just powering down their non-essential augmentations would make more sense? Obviously there are people in the world of HR with augmentations which are kind of like prosthesis, so essential functions would have to be maintained.