in event of subsequent abuse the stores want to ban an organization

A corporate shouldn't get to be the gatekeeper of anything - regulators / courts in a democratic system should decide such things so that the corporates can't abuse their position against a smaller entity. And CAs should be held accountable by the regulators too - a simple regulation like asking CAs to collect legal ID and certificate of registrations before issuing certificates to any person or entity can take care of this. Thus, if any illegal ill-practice is detected in any software, the regulators or the law can be informed and the developer / entity easily identified and necessary legal action can be taken.