Not sure I agree. After all, it contains materials that had been freely and publicly available at some time in the past. If a company produces a brochure which a library collects, does that company have a right to ask for it to be discarded just because they say so? I don't think so.
It was interesting to read that law firms use the Internet Archive as a resource in trademark cases--sort of a cheap and easy discovery process alternative.
Personally, I hope this case gets thrown out. I am definitely rooting for the defense here.