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.