That having been said, its hard to think that they were in compliance with 17 USC §§ 512(c)(1)(a)(ii) - (iii) in particular. Continued safe harbor protection requires that mega-upload:
(i)
does not have actual knowledge that the material
or an activity using the material on the system
or network is infringing;
(ii)
in the absence of such actual knowledge, is not
aware of facts or circumstances from which
infringing activity is apparent; or
(iii)
upon obtaining such knowledge or awareness,
acts expeditiously to remove, or disable access
to, the material;
I think it falls to a jury to determine if a 'reasonable person' would find that infringement was apparent to the mega-folks, but I don't think the "golly gee sucks, I just didn't know" defense is going to get them very far, especially in light of the emails in the indictment.