If the companies are signing all of their apps under the same cert then it's kind of on them for being stupid to sign critical internal apps with the same cert they use to sign these privacy violating apps; but if Apple is globally disabling all enterprise distribution certificates under the guise that the companies violated their developer agreements and NOT disabling their user-facing apps then it still seems to me they are engaging in selective enforcement.
Regardless of how I feel about the ethical questions involved, I don't think this skirmish will end well.