The Chinese government is telling the world with this attack that, if you choose to interfere with Chinese sovereignty by means of the Internet, or to enable those who would do that, then there’s a cost.
Note the way the attack is targeted. It’s not just an indiscriminate DDoS of Github, although that’s been the effect — instead, they’re aiming specifically at two repos whose content, being designed and built with the aim of circumventing the technical means by which are implemented a significant goal of China's domestic policy, enables no more or less than a direct attack on the sovereignty of the Chinese government.
To use that content is to say: "You may not run your country in the fashion you choose, because it does not suit me that you should do so."
To host that content is to say: "In this matter, we take the side of those attacking the sovereignty of the Chinese government, by making it easy for them to share and improve the tools with which they do so."
What you're seeing, then, is the quite reasonable response of the Chinese government to these statements. Yes, it's annoying for those of us who use Github, and no doubt it's much worse than merely annoying for those who administer Github. That is the point. Github is being encouraged to consider how much it's worth to them to maintain the stance they've implicitly taken in this matter. I'm looking forward to seeing how they respond.
As one of the billion people who live inside the Intranet "protected" by the GFW, I guess I can say I'm quite aware about how and why this happened. Let's start from the beginning.
For those who host things Chinese govt doesn't like, it usually just block the website altogether (Twitter, FB, and recently Google). But it had tried to block Github, twice. Each time there is a huge response from the Chinese webizens (mainly programmers) calling to unblock it.
Another way to block certain content from a website is to filter by keyword (like Wikipedia). But GH is encrypted so that's a no. The govt even tried to use some fake SSL certificates to MITM it. So some "smart" guys exploited this feature and created the repo greatfire/wiki and things like this.
Then some evil guys from GFW thought of this way, directing the attack at these user accounts, to warn GH to remove these accounts.
What I don't agree with you is the word "reasonable" (and the "no"). First, it's never "reasonable" to DDoS attack a website. Second, if you can't block the content, you have a choice to block the website and take the bitter from every single webizen against you. Finally, I believe it's the website owner's choice to choose who / what they want to use their website. Since GH is a U.S. company (I guess), it doesn't have to listen to a sh*t from the Chinese govt.
And of course it's up to the website owner whose content they host. They don't have to take down those repositories. But, unless the DDoS stops, they have to choose between taking down those repos and continuing to stand the gaff.
If I were to stand on a sidewalk outside of a church with signs saying "You're God is false, Heaven doesn't exist, you're going to die and disappear forever," and a parishioner decided to punch me in the face to stop me, they would be in the wrong, not me.
How totalitarian.
None of these thoughts is tremendously controversial in its own right, save where they conflict with cherished beliefs which I do not happen to share.
Reality is that political power extends from the barrel of a gun. But we also dream bigger and imagine better.
Github is a US company that hosts their service in US, Chinese government cannot possibly have sovereignty over that. If you believe there is righteous reason behind it, then you are supporting internet terrorism.
(The problem with rhetoric is that it can point both ways. Study the definitions of "sovereignty" and "terrorism" in international law, then try again.)