The guilty inocent thing is tricky, especially if you take the spirit of the law as opposed to the letter of the law. It is clear that the majority of Meguploads activity is the uploading and downloading of pirated material (I don't think anyone is seriously contesting this) and while it maybe legally dubious to take them down the fact that they were profiting massively from the indirect distribution of vast amounts of pirated material is also legally dubious.
It's the whole two wrongs making a right argument again, but I really don't see how anyone thinks the death of mega upload is a serious blow for freedom of the interent. If the US government were targetting twitter and other such services that allow individuals and groups the platform to express themselves I would be concerned. I can't seem to get myself all upset over them turning off lots of peoples free movie and pron pipe.
They removed copyright material as requested. I don't think they can do much more.