As for the NCAA option - I think the problem is that it is outside their jurisdiction if you will. Maybe they can get them on an APR violation.
As for SACS, they probably will look into it and they along with the university are the logical "police" of this issue.
What becomes problematic is the rules of the university and SACS accreditation guidelines.
Directed studies and directed readings are clearly allowed. The NYT article was a bit misleading when it talked about these as true independent studies. More likely, Petee set up directed readings courses that multiple students signed up for. All students in the course would read the same books articles and have the same assignments. I've offered directed readings courses and this is typically the approach that is used.
What is puzzling is how he was able to offer so many. The courses must be added to the registration system to be offered. They might be something like SOC490 which would be a generic course number for any directed readings course (e.g. there could be multiple and different SOC490's in any given semester). Some administrator had to have oversight either approving the courses or at least getting reports each semester about how many were offered.
The courses themselves may not be the problem (allow some are likely not sufficient for 3 hours of credit - but this is a subjective evaluation). The two most troubling factors are 1. the number of these courses that any one student could take (up to 6 taken by one student). At the most, a student shouldn't take more than 2 within their major and 1 would be preferable. 2. The student that was allowed to add the course 10-weeks into the semester - no way it could be worth 3 credit hours.
I also have a problem with Gundlach (whistle blower). His intentions may have been pure but it doesn't appear that he exhausted the process within the university to protest what he considered to be a violation of academic integrity. Going to the NYT was a questionable and potentially damaging choice. Further, his seeing a football player being honored for GPA in his department when he claims he never heard of the student is not unusal. Assuming Sociology has several hundred students - it is not unusal for any individual student to be unknown to any individual faculty member or even department chair.
In short, it's not clear that violations of academic policy or accreditation have actually occurred. (likely though!