A recent article at InsideCounsel discusses whether your employees should have separate counsel during internal investigations:
At some point, almost every organization encounters questions of actual or suspected wrongdoing by its employees, officers or directors. When that scenario arises, it is time to launch an internal investigation to ferret out any wrongdoing and to take swift action to correct it. For most employees, cooperation in an internal investigation is a required condition of their continued employment. However, if the suspected wrongdoing turns out to have been conducted by one or more employees, the investigation may lead to anything from disciplinary proceedings against employees to criminal charges.
[via: Litigation: How to conduct internal investigations at InsideCounsel]