I see this question a lot in the technet forums:

“I don’t want to monitor the IIS on this server and have disabled the discovery, but the server wont disappear. How do I get rid of it?”

To resolve this you just need to open a Operations Manager Shell and enter: Remove-DisabledMonitoringObject

Description of cmdlet:
Removes all monitoring objects for which discovery is disabled. For example, if you created an override to disable discovery for a particular database on a database server, calling this cmdlet would cause the removal of this database from Operations Manager.