Course records should not be deleted in PowerSchool, however you can make any course "inactive" in your building's course catalog.
To inactivate a course, go to School Setup > Courses and click on the link "Manage Courses for this building". This will take you to a screen that will list all courses with checkboxes next to each course. To inactivate a course, uncheck the checkbox next to the course you wish to be inactive in your building.
After doing this, the course will no longer appear in course lists in your building.