a) potentially threaten GitHub's business (blackmail, disgruntled employee, internal threat, security services, concerned comments like this etc.)
b) real companies store their source code on GitHub; their source code is, at least, 50% of their business.
c) GitHub isn't really a startup anymore, they have hundreds of employees, you can't let that many people have unfettered access to data. Someone could loose a laptop...
d) As mentioned, Yahoo! was very careful with customer data
e) It's called a Private Repo
I'm making a big set of assumptions, you are right. I'll move my GitHub to my own server now... installing GitLab which I absolutely hate but it's better than trusting an unknown set of engineers.
I've just realised probably any Digital Ocean engineer can get root on my box if they want to right :-(