Hi Amanda

There are some suggestions of workarounds discussed in https://totara.community/mod/forum/discuss.php?d=16970 .

This involves hiding categories and applying a role that can view hidden categories to each category and then assigning the user to these category roles.

To improve on that you might want to add a couple of HTML blocks to the front page (or other pages - perhaps even as sticky blocks) and determine specific roles (new system roles you create - role user Dept A and role user Dept B) that can view these blocks. Then assign users from dept A to that role in system context.
In block A add direct links to courses for dept A and in block B for dept B.

Craig