It seems unproductive to society to treat "criminality" as a write-once binary switch, which once flipped can never be erased. There are far too many confounding factors. Someone is benefiting from the desire to brand human beings for life for something in their past, as well as the immediate assumption that accused is as good as guilty, but it isn't society.
In fact, I know someone who used to like Megaupload to an extent, but even before a trial, thanks to this cultural tendency and inflammatory news coverage, said, "It turns out they were guilty of racketeering and money laundering, so they were some pretty bad guys." Despite being a reasonably well-informed person, he too fell victim to the urge to equate accusation with guilt.
At this point it doesn't matter what Kim Dotcom did a decade ago in Germany, or whether Megaupload is guilty of all the things they're accused of and more. The damage to the public's perception of legitimate file sharing has been done, and what I think was the most important thing to come out of Mega, the MegaBox music service, is most likely dead.