The issue is not that MS obeyed the takedown as they are required to do. The issue the SFC are discussing is that MS are part of the group that issued the takedown request in the first place.

MS has two hats in the game here: one as a member of the RIAA who have issues a DMCA take-down request, and on as the owner of GitHub which has acted upon that order.

DMCA takedowns are about removing violations of someone's copyright, like posting a Beatles song on YouTube. Though the request was made to look like a takedown request, it's hard to see how they could make the claim the software itself was a copyright violation.