The correct way of doing this is to log in your Sitebuilder and choose to “Unpublish” it. The Unpublish button is listed under the Actions column on the main Sitebuilder page.
This will remove your Sitebuilder site from the account. Though the content will not be deleted and you will be able to work with it later.
In case you will not need the content at all you can delete it by clicking on the “Delete” button under the Actions column on the main Sitebuilder page.