(in reply to the much more nested comment) but this is the age of electronic data - it is easy to delete the content that was the subject of the DCMA and leave the rest of the site up read-only for a month while people archive (or something).
While I think the government could have been more forgiving of innocent third parties, remember that MegaUpload was a virtual company where all the computers were leased on the cloud. Those vendors were not being paid and meanwhile had capital costs on their equipment for as long as the prosecutors were copying off data. They deserved to have their equipment returned to them as soon as possible.
