To make a sales organization inactive without losing leads, deals, and customer date, a company admin can deactive the sales org users. To do this:
Click Your Roles > EPC > Sales Organizations and then "Roster" next to the sales org you want to inactivate.
Click into a user, scroll to Admin Settings and click the box next to Inactive. Then click the blue Update Profile button. This will change the user's status to inactive so they can no longer log in.
Do this for each user in the sales org.
To completely remove a sales org, return to the Sales Organization menu and click the red trash can to remove it. Note, removing a sales org this way does not preserve deal, lead, or customer data. All information will be lost and cannot be restored. Only delete sales organizations if you are sure you no longer need any data.