I attempted to remove AD CS from my dedicated 2008 R2 Enterprise Root CA server today in our test environment. It succeeded with the following warning (I stripped out company specific stuff):
Warning: Setup was unable to delete Certificate Enrollment Web Service information from the Certification Authority object in Active Directory Domain Services (AD DS). To complete Setup, delete the information manually using the command: certutil -config"<domain>-<server>-CA" -enrollmentServerURL https://<server.FQDN>/<domain>-<server>-CA_CES_Kerberos/service.svc/CES delete. Catastrophic failure Unexpected method call sequence. 0x8000ffff (-2147418113)
When I run that command in a cmd or ps window it get the following errors:
CertUtil: -enrollmentServerURL command FAILED: 0x80070490 (WIN32: 1168)
CertUtil: Element not found.
Permissions is not an issue (Domain admin, Enterprise admin), I've rebooted the CA server. I restored this from a backup into our isolated test environment, along with one of our DC's.
I've seen a similar post elsewhere on TechNet (Exchange forum) but in his case the recommendation was to re-install Exchange.