my reading of mega's brief and the government's response, is that the government did not ask mega to preserve any data. Rather, the warrant, served against carpathia, was sealed, with exception for disclosure to mega for compliance with keeping the existence of the warrant secret. Mega's brief includes the original email from one of carpathia's directors, which states that the government wants the files themselves to be turned over, and recommends that they be aggregated onto one or more drives from the server, then those drives be handed over. It also recommends that mega not start an 'E7 ticket.' I have no idea what that is, but the implication is that opening one would alert the ninja users as to the reason for the unavailability of files.
The brief says that mega maintained the files publicly available in keeping with the government's express desires, but the document they offer in support shows no such government request. In fact, the government did not interact directly with mega, as the warrant was being served directly against carpathia, as the actual hosts of the files. There seems to be a lot of 'the government request is well documented' going on in the comments here, but its not evident even in mega's own supporting documentation. The government seems to have gone out of its way to preclude such a claim simply by not interacting directly with mega.
Furthermore, the affidavit supporting the domain seizures in early 2012 was not, as one might infer from mega's rhetoric, based exclusively on the files at issue in the ninjavideo case. In fact, one of the two infringing files specifically named, with URL, in the affidavit was twilight breaking dawn pt 1, which had not been released in 2010 when the gov was pursuing ninja.
The problem with the whole thing, in my opinion, is that mega could have made a decent argument that they couldnt remove the specified files from public availability without giving the ninja users cause to ask why, and that in order to comply with the spirit of the seal on the warrant, keeping the files up and available was the only real option. The main weakness in this is that for only 39 files, 'random server shenanigans' would be totally par for the course if they'd just taken the files down with no explanation. Server errors happen. This argument also only goes so far without either a very official letter of understanding from the DOJ that mega would not be held liable for infringing copyrights while complying with the warrant, or even better, an injunction mandating that they keep the files up and remain silent as to why. But that's not what happened. A sealed warrant was served on mega's host, carpathia, apparently seizing the files and compelling the disclosure of identifying information on the ninja users. That's not really the same thing as 'complying with a documented request by the DOJ to keep breaking the law.'
I'm sure there's a bunch of stuff i'm missing, the suit is pretty complex at this point. Even just mega's brief includes both mega's action as well as a third party action to compel the DOJ to release private, non-infringing data back to private mega users. But the entrapment claim seems kinda stupid. Copyright law needs some major reform, but in the statutes. Letting Mega off will accomplish as little as convicting them, imo. Either way, a bunch of other file lockers stepped in to fill the void, and the copyright system will still be a statutory nightmare essentially legislating the corporate content creation model of 20 years ago. Oh, last note, Wired's story has good links to the briefs, affidavits and warrants discussed above, much better than TFA linked above.