Someone at Atari simply doesn't know what the hell they are talking about.
I would reply that none of the archives being hosted contain any copyrighted code and ask her to clarify.
the the reply
They're not protecting the copyrighted code/bios/games. What they're going after now is the use of the name atari. 'Atari 7800' for example is a copyrighted name. By using it as the title of a webpage you may be in violation of their copyright.
It would never hold up to any scrutiny, but it makes for good scare.