512(c)(1)(a)(ii) has the so called "red flag" requirement. "n the absence of such actual knowledge, is not aware of facts or circumstances from which infringing activity is apparent"
Essentially, if they know about a fork and a reasonable person would know it is infringing, they lose their safe harbor.
Does GitHub have in house counsel? This policy is risky and doing it response to an outcry about actual pirate programs this will look horrendous if they end up in court.