Looking at the challenges, it would be cool if GitHub picked that up and published best practice guides for teachers and also collaborating researchers. Such guides could come from this study and others like it. I remember they're doing research on how researchers use GitHub already.
Oh, now I see they actually interviewed John Britton from GitHub on that. I don't buy this completely, though:
"But as far as...we don’t have a set, like, this is the way, right? There are multiple ways to use GitHub in the classroom, and it depends on what goal you’re trying to achieve."
Same is true for software development, yet they promote the GitHub Flow. Find the practices that work for 80% of the people / contexts!
Interesting. Interviewee can't use GitHub for their class because the servers probably are in the US: "Copyright is a big issue. For instance, we are working with a novel. In Canada, that novel is in public domain so it can be accessed online, but not in United States."