They're all taken down already. Forks are a̶u̶t̶o̶m̶a̶t̶i̶c̶a̶l̶l̶y̶ manually enumerated by the DMCA'er and removed
Any centralization is fragile. Github is more fragile than what is possible, but there is little point on improving that.
I'm sure that you could rm the .git/ and overwrite it but keep it pointing at the same repo. I don't know what would happen on the remote, though, when you push.
For good measure, you should also probably run a `git gc` (garbage collect) on the repo too, just to be sure. :)
Not from my computer.