If you don't want a department to show up in the site map, you should add the department to an inactive category.
To place the department in an inactive category:
1. Editing a department can be completed under Content Departments Edit Department
2. Click +Settings to open that section. Choose an inactive category from the List Under Which Category Heading drop down menu. (Work Pages is always a good option)
3. The site map is rebuilt once per night so the changes will not be reflected instantaneously.
*If you want the changes to take place immediately, you can run a manual site rebuild.