You can do this -- it is not immediately clear how as it is named different from the GUI, but this is what you'd do if you have an addin of ID "com.mycompany.jmpaddin"
Names Default To Here( 1 );
addin = Get Addin( "com.mycompany.myaddin" );
addin << Unload // to "unregister"
addin << Load // to "register"
I don't see any documentation for this though, got it through trial and error...
And just to state -- unloading an addin does not get rid of any namespaces / classes / global variables set by the addin. It just get's rid of any menu customizations and prevents it from loading when JMP starts next.
Jordan