Appmon agents are loaded into the process of the technology you are monitoring. To stop them you need to shut down the Java application they are running inside and then if you wish to start the application without the agent starting up again, you would remove the jvm command line arguments to load the agent.
In appmon you can always change mapping in agent group, and restart collector. Or configure restriction in license settings to exclude particular agent group from monitoring (again, restart collector). But this will stop collecting metrics and purepaths but will not turn off agent itself. To take it down from application process you have to delete configuration that is injecting it (for web servers, processes).