Is the auditor really threatening disqualification without saying why? What do you mean by "We refuse to acknowledge any disqualifying defect"? Do you mean that the auditor has pointed out what he considers to be one or more plan failures sufficient to disqualify the plan but that you refuse to accept that they are failures?
Presume, please, that whatever agony the IRS would have to deal with to disqualify the plan is nothing compared to what you would have to deal with if they did.
Disqualifications may be rare, but it is not because the IRS is unwilling to push that hard. If they are rare, it is probably because most plan sponsors will realize that going through audit cap would be less expensive and disruptive than if the plan were to be disqualified so they agree to go through audit cap.
Have you engaged the services of an ERISA attorney to help you? It might be a good idea.