You might be interested in a similar question I had asked about what to do with course materials from term to term. There were several proposals, but the cleanest option appears to be creating new organizations for each year (or semester) that a course is taught. This is my plan moving forward.
In regards to the courses themselves, I always use a different organization for each course. This is, in part, because the course materials include lessons, exercises, etc. and it is already a bit tricky to keep the students from getting confused with all of the different repositories in a single course. Hope that helps!