Auto-deployment of the SimpleMDM mobile app can be disabled when creating a new device group by unchecking the option labeled "Auto deploy SimpleMDM app".?
You can also disable deployment to multiple device groups that have already been created from one screen. The SimpleMDM app is deployed the same way as any other app is: through an assignment group. By visiting the Assignment screen under Apps & Media, you can remove any assignments that exist for the SimpleMDM app.