Until version 184.108.40.206 it has not been possible to physical delete sites. When a user deleted a module entity, the site was marked as deleted and hidden.
This feature changes this, as administrators can now go to "Site Maintenance" in WorkPoint administration. This works as a "recycle bin" for sites that has been marked for deletion.
Here you can review and delete sites. When there is a lot of sites, you can run a job to delete them.