Any chance of seeing another doctor? It sounds to me that your current dr is being a bit unfair. I know it is very difficult to go and tell someone new about it all again. However if you felt able to do this, perhaps they would be willing to write something to certify that during that time you were too ill to attend class.

I guess I have the view that the less school, university, work knows the better, but that is purely personal and perhaps seeing the school counsellor would be the other most productive step

good luck