github went way above-and-beyond here. It is under no obligation to:
1) Enforce an invalid DMCA request
2) Take down forks and repos from other users, without DMCA requests
3) Threaten to ban users
DMCA has a simple, neutral process. github receives a request. It's required to take down that specific tool if it's a valid request (NOT everyone who forked it). The developer who owns that repo can then put that up. At that point, github brings that repo back, and gives the RIAA means to file litigate against the developer. It's inspired by the concept of a common carrier, where github would be acting as a neutral party, not a thuggish policeman-for-hire.
If github ignored DMCA requests, I wouldn't do business with them either. I expect them to be a neutral third party, as the law dictates.
What github did probably wasn't illegal either. Most companies can fire a customer for no great reason, which github did.
A perfectly reasonable response, I suspect, might be to start sending github large numbers of inane takedown letters similar to the RIAA one, alleging that random tools can circumvent copy protection. For example, vscode, cpython, and many other projects live on github, and can be used to circumvent copy protection too. That's a true statement.
github is welcome to ignore those letters too, since they don't conform to DMCA requirements. Or they can follow them.
In either case, I'm kind of curious what github would do. I suspect if they randomly kill projects, most projects will go somewhere else. github won't be considered a reliable service provider. Or github will re-evaluate their policies to be more reasonable, and not take down projects willy-nilly, which would be a good outcome too.