Removing desktop pool entitlements or deleting AD accounts does not remove users from a desktop. To clean up the environment, have you looked at PowerCLI to do it?
Thanks for the reply, mhampto. We are able to manage all other aspects of pool entitlements and VM assignments via PowerCLI, just not removing stale user IDs from the global entitlements in Cloud Pod Architecture.
The Cloud Pod Architecture ADAM DB is not exposed to PowerCLI (at least in 6.2.0 that we're on), so there are no other management commands outside the lmvutil commands I mentioned in the OP, which fail.
For anyone (especially VMware folks - hint, hint) that want to recreate the failure/bug in your lab:
1) Initialize Cloud Pod Architecture in your View Pod
2) Create a new desktop global entitlement
3) Create a new AD user in AD
4) Add the AD user to the desktop global entitlement
5) Delete the AD user from AD
6) Attempt to delete the non-existent user from the desktop global entitlement using the lmvutil command from my OP
lmvutil.cmd --authAs [admin account] --authDomain [domain] --authPassword [admin account password] --removeUserEntitlement --userName [domain\user ID] --entitlementName [global entitlement name]