I'm not sure all the things you list as being possible are true.
- Every GitHub Repository could be access by anyone as if they had full administrator privileges.
- This means that anyone could commit to master.
- This means that anyone could reopen and close issues in issue tracker.
- Even the *entire* history of a project could be wiped out. Gone forever.
As I understand it from his explanation[1] he added his public key to the Rails user, which has permissions to push/pull to the repository. This doesn't mean he had web administrative access, just Git access, since you cannot log in to the web service using your private key. I hope that's the case, at least.
[1]: http://homakov.blogspot.com/2012/03/how-to.html