Maybe you could try making your training program a Commodity as described in Libraries RKRM.
You could use the Commodity to let the mouse information though to Intuition when you need to, and you can also use it to swallow mouse messages and supply fake messages when you need to as well.
Perhaps it can be installed when your tutorial runs. It would wait for instructions from your main program in the form of exec messages (ie: enable_mouse, disable_mouse, insert_event, quit etc)
After the tutorial part, the Commodity can be shut down.
