What I don't get is why they didn't inject a script into all html passing through the firewall. That would have achieved a much greater effect if they really wanted to take out GitHub - the Baidu Analytics tracker is just a single script.
This is just my theory: I think that GFW is currently entering its next stage, which probably includes MITM attack to TLS traffic and some attack specific to websites outside China. I suppose that since everything now is in a "research" stage, they are just trying to see if the technique works and how much it could go.
Disclaimer: I was an user inside China and being blocked from the real Internet. So please take my words with a grain of salt.
Everybody's talking about how this is a targeted attack against GH, but I'm starting to think you might just have hit the nail on the head...