My interpretation of what happened is that Ms. Reid's lawyers requested that specific posts within a full archive be removed from the archive. In other words, they weren't asking for removal of the entire archive. They just wanted a "sanitized" version to be accessible to the public.

The Internet Archive has a mechanism for doing this, as I understand it. It involves asserting copyright over the material in question and essentially "making a case" for removal. IA decided the case they made didn't pass muster, and denied specific removal on those grounds, which is why they mention "journalistic nature of the archive" and so forth.

But that's entirely orthogonal to their policy of treating active maintenance of robots.txt as indicative of positive copyright assertion over the contents of an entire domain -- which Ms. Reid's team appears to have taken as a fallback position. They couldn't get the sanitized archive they wanted, so they just made the whole thing invisible.