But on the other hands, Github is a popular site, and it attracts many users so people can spawn lots of PC to create mass attack. Why not? It's a popular site so they want to test how well their tools can keep up with GitHub. People would assume that as of today, 2012, operation engineers have learned enough to protect and recover from DDOS.
GitHub team did a very good job recovering. Not bad. But certainly the infrastructure is still not able to handle such DDoS. GitHub needs to invest more money on that to secure service.
Whatever the reason might be, it's not necessary to speculate. In some movies, we even had banks / investors hired others to crack their own banks or stores next to the bank to destroy critical evidence (financial loss). That's a scam. Maybe we should speculate if it was GitHub's own DDOs? God knows. Everyone will call me crazy if I believe in such thing. No I don't think it was GitHub, but let me remind everyone these strange things happened before in both fiction an real life. But the point I want to make is no one knows and it shouldn't matter.
Whoever attacks it is not important at all. GitHub will learn from this and make the service more reliable.