Principal is violating the rights to education of my nephew

My nephew is doing grade 12 at Magigwana High School in Mpumalanga Province, we never heard of his bad behavior or ill disciplined manner. To our surprise mid year he was told to leave school since he is a below average learner. The principal cited that he will affect his 100% pass rate. We then went to the school to have a discussion with him after several telephone conversations which did not yield any positive outcome. During our meeting the principal mentioned that the learners is well mannered, attend school and very focused but his performance is not satisfactory. As parents we asked what initiatives did the principal take to assist the child? After lengthy discussion the principal apologized and the learner was allowed back at school. 3 months later the learner was expelled for going to the clinic during school hours after vomiting in class. The learner did ask for permission to go to the clinic but the teacher refused.

I believe that the educators are supposed to be more supportive instead of mistreating a grade 12 pupil. I am currently informed by the pupil that the principal has submitted only 3 subjects to Department of Education, is it allowed?