If you find the closure of Megaupload troubling, just read the indictment. I won't consider the legal matters here, but the emails cited in the indictment paint a pretty clear picture of intent. They show that:
A) In many cases, Megaupload employees knew that *specific* files on the site were in violation of copyright, but they took no action to remove the content
B) Knowing specific files were copyrighted, megaupload still paid out rewards to those files' uploaders
C) In a few instances, staff members shared links to copyrighted content with eachother and with the internet at large.
Those are just the most egregious points, which basically demolish their claim of safe-harbor. But there's more: The claim of conspiracy at first sounds ridiculous and overblown, but it begins to make sense when the indictment describes all the ways Megaupload is alleged to have actively worked to conceal piracy. Claims of DCMA compliance are shot to pieces by an allegation that certain links were the subject of takedown notices, but remained active for over a year. I could go on, but just read the thing yourself, it's actually pretty interesting for a while.
The guys at Megaupload sound hella guilty. The only other explanation is a massive conspiracy involving the FBI and the Justice Department, but I have trouble believing that.