While in Grad School, students are earning a stipend, sometimes as much as $2500/month. This is justified because they are paid through the funding of their research. I see no issue with a small monthly stipend in addition to the other benefits. It's not like they could get another part-time job.
The research is what they are being paid for... so it is a "job" that happens to associated with the degree.
I doubt there is anything in the NCAA guidelines that would prevent an athlete from doing the same... i.e. actually performing the research/work.