I completely understand the concern about defensive reactions - I agree with Richard that working directly with the respondent to determine root causes can be beneficial. In some cases, I have actually seen this make people LESS defensive as they have the opportunity to help find the root cause instead of feeling like they are being accused behind their back to their supervisor during "private" meetings.
I tend to lean toward the "transparency" approach whereby keeping communications open, as much as possible, brings a greater element of trust and understanding in the positive goals of an audit process.
Regardless, the stress of an audit can always cause some defensiveness from respondents and auditors are always challenged to develop a positive rapport throughout the process to assist in creating a cooperative culture to reduce the "we/they" syndrome which can easily occur when individuals know they are being reviewed.