Yet companies ignore DMCA complaints all the time.

Github is unusual in my experience in that they act on even transparently fraudulent DMCA notices (I am reminded of a few years ago where they took all of Mozilla's repost offline because of a obviously bogus DMCA complaint filed by a intern that was furious that their changes weren't merged or something along those lines).

And while copyright penalties look pretty stiff, they're pretty non-threatening compared to ordinary state product liability-- which is almost completely non-disclaimable. Liability is just one of the consequences of doing business.

I certainly wouldn't suggest that Github should be ignoring DMCA complaints as a general practice (though plenty of providers sure seem to do so), but in this case I think they could make a calculation that the risk might be worth it: I know quite a few parties that have moved off github as a result of this incident.