How to delete a Control-M/Agent using a command or script so that it no longer appears in the Control-M Configuration Manager and the Control-M/Server database?

Method 1:
​​​​​​Use the command ccmcli from the Control-M/Enterprise Manager account with the option delete_agent
Example:
Suppose you have a Control-M/Agent with node name myagent with name ccmagname under Control-M/Server mydc, then this command syntax is as below
em ccmcli -u <emuser> -p <password> -s mydc -t CTM_Server -n ccmagname -cmd delete_agent -node_id myagent

It will remove the Control-M/Agent from the Control-M Configuration Manager and from the Control-M/Server database.

Method 2:
Use Control-M Automation API service of "config server:agent::delete" which will remove the Control-M/Agent from the Control-M Configuration Manager and from the Control-m/Server database, and its syntax is as below
ctm config server:agent::delete <ctm> <agent>

For detail, please refer to the Automation API guide 
https://docs.bmc.com/docs/automation-api/918/services-783053199.html
 

The following video demonstrates this solution: