How is it okay for source code that enables infringement but does not infringe itself to be taken down by a DMCA request? The claimant in this case doesn't own any of the rights to the software yet wants it removed anyway ...
You have to squint and let the screen go a bit blurry to see it, but I wouldn't count on getting a judge that sees it the other way if I was GitHub. I've always interpreted "access controls" to mean a specific "technological measure" such as CSS encryption, but in a very broad sense the law does allow for tools that don't have any particular copyrighted works in them to be considered illegal and rulings that would disallow their dissemination.