From my understanding, the government will have to show that: A) That the purpose (or at least one purpose of the site) was to aid copyright infringement (or other illegal thing) B) That this guy knew about the purpose, even if he tried to pretend he didn't. I'm guessing that they won't have any problem convincing a jury of (A), and he emailed someone a screenshot of his computer watching a pirated video on MEGAVIDEO.COM, so I don't think they'll have much trouble with part (B), either.
I don't think they have to prove actual knowledge if your activities facilitated the crime. I think they need only prove a lesser "subjective test": that is "would a reasonable person have known that their work was facilitating crime?". This kind of reasonable person test is commonly used so that people can't use a "blind eye" defense. Willfully turning a blind eye to criminal activity doesn't absolve you if you were actively participating.