Try this -
Go to CallManager>User>Global Directory>(and find the user)- click No ICD Extension.
Then go to CRAA>Subsystems>ICD>Resources. Set resource group to -Not selected-, and click on disable and update.
Go back to Resource list, click on Inactive Agent link. The user should be there for deletion. If not, may need to wait for server to sync, for us that's a 15-20 minute wait. Not sure what your time frame would be for auto sync.
Nat