I think it's in Github's interests to push back on this. MPA's dubious legal requests likely cost Github time, money, and PR to resolve properly. It adds up over time and I doubt any company wants to be caught in the middle of an arms-race conflict like this, nipping it in the bud could very well be worth the upfront legal fees.
I imagine MPA would also be emboldened by this if Github removes the Nyaa repository forever on what is basically a pretty flimsy basis ("Nyaa.si uses the code and that's a piracy website so the code itself is piracy").
