Right, it's black and white that they ignored copyright violations on a bunch of files. But that is not the same as encouraging infringing files over non-infringing files, or asking people to upload infringing files.

If you uploaded a popular infringing file, you might get $100, or you might get disqualified.

If you uploaded a popular non-infringing file, you would definitely get $100.

Megaupload knew about some of the piracy. That does not mean they arranged it. They treated it like any other file.

Also keep in mind that an indictment is designed to make the indicted party look as unsympathetic as possible. There may be additional context given which turns those e-mails from "smoking gun with Dotcom's demonic fingerprints" to just "Viacom vs. YouTube-esque questionable behavior" if that case ever goes to court.