When you create divisions, they will persist throughout all of the seasons you create. However, if you do not have teams in those divisions in a given season, that division will not show to the public.
Because divisions persist throughout all seasons, you cannot delete a division from one season and leave it in another. To delete a division, it must be deleted entirely from the site.
This means, that in order to delete a division, all teams must be removed from that division in past, present and future seasons in the website. When done, you will find a red delete button to the right of the division name and this will delete the division.