Is Github expected to take on personal liability for every repository it hosts, and provide free legal representation for their owners in court? I don't know if that's a winning business. Following the DMCA is probably a smarter move, which means taking down the repositories when a claim is filed, and restoring them 10 business days after a counternotice is filed.

Several of those counternotices were filed at the very end of last month, and the 10 business days have not yet elapsed. Github can't put them back online early unless it wants to lose the liability protection.