Actually the takedown wasn't mandatory because (AFAIK, IANAL, etc) it wasn't actually a takedown request that GitHub received. Takedowns only apply to infringing content itself, not to tools. (Even if the tool were in violation of the DMCA it doesn't seem like the RIAA would have standing to pursue it.)

That being said, it also seems like GitHub is well within their rights to choose not to host a project accused of violating the law.