Removing a 2000 server with certificate authority from the domain

I have an issue with a 2000 server which has lost it’s trust relationship with the domain. My inclination is to remove it from the domain and rejoin to clean up the mismatched AD entries. The problem is that it’s arunning certificate authority services to facilitate ssl access to it’s SQL database from a few specific IP addresses. I can’t remove it from the domain with certificate services running. Anyone have a step by step process for disabling or removing cert services so I can fix the domain issue?