After Nat's cynically duplicitous comments and actions, it's hard to view this as anything other than PR. A $1 million expense is not a big advertising expense for github. It was a $7.5 billion sale. Microsoft spend 0.013% of that on this PR piece.
I can't imagine the fallout from this didn't wipe several times that off of github's valuation.
If github had done this before the EFF letter, it would have been something else. With the EFF letter, they have zero liability to reinstating the repo, and are borderline legally required to do so.