Some people think RIAA’s DMCA notice is not legally valid, arguing RIAA is not the copyright holder and there is no infringing material. DMCA takedowns are for taking down works you own the copyright to; not for enforcing any arbitrary aspect of legislation.
It’s my understanding that service providers do not need to comply with illegal requests.
For example, if I DMCA’d <an oil producer>’s repository on accused violations of environmental protection acts, I don’t think it would be taken down, would it?
If GitHub was an independent company advocating for open source; would it have acted any different?
Note: Microsoft is a member of the RIAA.
Apple made waves and built lots of favour for resisting the FBI and challenging quasi-legal processes. They took risks and demonstrated their principles (Suing the FBI over a terrorist’s iPhone is unlikely to be the first recommendation from their legal counsel).
This smells like a qausi-legal process, and it would look great for GitHub/Microsoft if you do.