If you already associated Mojo Helpdesk account with your Google Apps domain, but want to remove that association, you have to do 2 things:
1. Login to your Mojo account, go to Manage -> All settings ->
Configure Mojo Helpdesk -> find 'Google Apps domain', click on the
remove link next to it and follow the process.
2. Login to your Google Apps account as admin user, go to your
Dashboard, click on Mojo Helpdesk application, then click on the
link next to 'Delete application'.