I think that it is very important that, when you explain the rationale for your decision to the supporting auditor, that he understands why you made your decision. Most people will respect the lead auditor's decision, even if they do not agree with, if they understand why. So, he does not feel that his input and findings are being disregarded for spurious reasons, such as company politics. The easiest way to alienate a good auditor is to give them an impression that what they find is not valued and you can simply use your authority, as the lead auditor, to dismiss their comments.