"I think you will find this course as not a vocational course--not primarily a vocational course--but an intellectual course about how things really work."
what does intellectual course mean? what the difference between intellectual course and vocational course?
So this course description would be clearer if it had said "I think you will find this course to be not a vocational course"; or (better, I think) '... you will find that this is not a vocational course'.
Now - to answer the question! An intellectual course is one that involves and requires use of the intellect; a vocational course involves practical training in a skill required for a career.