Obviously it hasn't been proven, because the case hasn't been taken to trial. But the indictment is damning; the DOJ has MegaUpload's emails and lays the case out in Kim & Co's own words. For instance:
On or about April 23, 2009, DOTCOM sent an e-mail message to VANDER KOLK, ORTMANN, and BENCKO in which he complained about the deletion of URL links in response to infringement notices from the copyright holders. In the message, DOTCOMstated that “I told you many times not to delete links that are reported in batches of thousands from insignificant sources. I would say that those infringement reports from MEXICO of “14,000” links would fall into that category. And the fact that we lost significant revenue because of it justifies my reaction.”
And:
* When an outsider complained that MegaVideo's hosting of the Showtime pay-tv series "Dexter" had desynchronized audio/video, instead of taking down "Dexter", Kim Schmitz fired off mail saying that fixing the AV problem was a priority.
* Mega employees themselves uploaded copies of major motion pictures to the service, such as Luc Besson's _Taken_.
* There are Mega emails, on which Kim is apparently CC'd, in which employees enumerate the specific files uploaded to certain high-performing affiliate members, noting (approvingly) that they include copyrighted movies and TV shows. For instance, one line item in an accounting mail: 100 USD [USERNAME DELETED] 10+ Full popular DVD rips (split files), a few small porn movies, some software with keygenerators (warez)
There's a widespread misunderstanding of the DMCA on Hacker News and Reddit, and that misunderstanding goes like this: "to follow the letter of the law, you must somehow be responsive to individual takedown requests from rightsholders". That is in fact not correct; it only captures part of the responsibility of service providers under the DMCA. Another responsibility, clearly spelled out in the DMCA, is that you can't operate a service with knowledge of specific infringing content. You cannot know that Luc Besson's _Taken_ resides on your service at a specific URL and then simply wait for a rightsholder to request its takedown. If you operate your service knowing that there are specific pieces of copyrighted content on your site that you're "getting away with" having because nobody's sent you a takedown, and a prosecutor can show that (for instance, with an email obtained during discovery in which your staff does a line-by-line accounting of a promotional program you ran in which you paid contributors to your site to upload copyrighted material, and in that email you specifically make a case for paying one such prolific uploader more because more of their material is copyrighted), you forfeit safe harbor protections.
Finally, and orthogonally, let me just add that while we can't convict Kim Schmitz on the presumption that he is a scumbag fraudster, and the checks and balances in our system of government do require us to dot every 'i' and cross every 't' with regards to chain of custody of evidence, evidentiary standards, and cause for search --- so that if Schmitz escapes his inevitable imprisonment this time, I'll at least be comforted that our legal system takes those issues seriously --- Kim Schmitz gets no such pass in the court of public opinion. The evidence against him in that court is overwhelming. Unless you think the DoJ fabricated his emails, we know he's a crook. You can pretend there's a controversy here, but if you do, my take is you're not allowed to criticize Zynga or evil hedge fund managers and HFTs anymore.