A Google admin for the OU who is also an admin on the License for the Don Johnston tool can remove the OU.
1. The admin needs to log into the tools website.
2. Select, "Manage Students".
3. Select, "Organizational Units".
4. Click on the Trash can to the right of the OU you want to remove.
5. Select Notify me if you want to know when the OU has been removed from the tool. ( You will be sent an email when the OU has been removed.)
6. Click on,"OK".
It may take a few minutes for the OU to be removed. You will need to log out then back in to see the changes after the sync is complete.