Below are the steps necessary to stop monitoring a cluster that will be decommissioned and is currently being monitored with System Center Operations Manager 2007. If you do not follow this procedure, there is a risk that you may have orphaned virtual servers after the cluster is decommissioned.
In order to remove monitoring of the cluster, perform the following steps:
1. Remove the Operations Manager agent from all nodes of the cluster being decommissioned.
2. Ensure that all of the cluster nodes (including the virtual cluster nodes) are no longer visible in the Operations Manager console by checking the Agent Managed and Agentless Managed views under the Administration section of the Operations Manager console.
3. Proceed with decommissioning the cluster.
Note: This information was originally contributed by Adrian Doyle, Program Manager, on the Operations Manager Support Team blog:
http://blogs.technet.com/operationsmgr/archive/2009/10/01/how-to-decommission-a-cluster-monitored-by-system-center-operations-manager-2007.aspx
After scom r2 cu1? i believe this scenario isn't possible anymore. However you might run into an issue where a cluster and its physical nodes are decommissioned, but you can't remove the agents (clusternodes) from scom as scom still thinks it is managing a cluster.
As a workaround you can override the cluster discoveries for those agents and then use the "Remove-DisabledMonitoringObject" cmdlet. After that the agents can be deleted.