If you want a student's transcript not to include a course, you can remove them per student (Here's how to remove a Course from All Transcripts).
How to Remove a Course From a Student's Transcript
- Go to Courses > Courses > Edit the appropriate Course
- Scroll down to the Registrations tab. Select the student then click the Edit Registration button.
- On the Edit Registration screen uncheck the Show on Transcript checkbox. Click Save and Back and you are done.