Yes, witness protection is very important. Again, this was one of the issues with the government commission: that there was ineffective protection of people who were providing testimony. It meant that perhaps a lot of people who would otherwise have been willing to testify simply weren't willing to take the risk.
A number of these commissions of inquiry have taken place across Africa and East Timor. I think the UN has a lot of experience in conducting these types of inquiries and ensuring that victims and witnesses to abuses are afforded adequate protection in testifying and in sharing their information.