(I never said that Megaupload is innocent though, but I like well followed procedures, they are the guardians of our liberties)
This article is really about the merits of the case, which is separate from the question of following due process upon arrest and indictment.
But if the FBI loses this case and its image is tarnished then it could be a precedent and may change the way these copyright infringement cases are conducted. I am not american and I would hate to see the FBI take away my startup business on the ground that I am violating copyrights because of my users.
The FBI will attempt to prove that MegaUpload was an illegal business. Why should they just let it keep running if that is the case?
IF they're found guilty, the additional time of operating in a situation where everyone who might want to use them to pirate knows they're under significant government scrutiny is not likely to make the damage done all that much greater.
As for destroying evidence, in this case the feds are happy to let the hosting companies destroy data - they've apparently warned Megaupload that lots of user data will get deleted by the hosting companies soon for failure to pay, because Megaupload's assets were seizes so they can't pay...
So not only are they not allowing the files to stay online, they're preventing Megaupload from ensuring they can retain copies of customer data in the event they're found not guilty.
Regardless of whether or not they're found guilty, this way of acting is downright disgusting.
If you allowed all organizations to continue to operate until they were proven to be breaking the law you'd have something very closely resembling anarchy. Imagine if ever pump and dump boiler room operation had 1-3 years advanced notice before being subject to asset seizures.
You can call technicalities and process and mandates and whatever, but the facts stand: Megaupload is dead, and there was absolutely no trace of a fair trial.
That's way too subjective for law. The prosecution has to prove to the jury (NOT the judge) that what they found is, in a criminal case, beyond a reasonable doubt, an illegal substance.
The ongoing damage here, if any, is only economical and a much more narrowly construed seizure could still largely prevent further damage while safeguarding their legitimate customers.
The comparison in this case might have the prosecutor go after some lesser charge just to stick anything in order to justify the huge operation in the first place.
Now, since as you say, this was a large multi-national operation, I don't know if all those charged will be extradited to the USA, or if they'll be tried in other countries. I really have no idea about laws & procedures around the globe, but if they are extradited to the USA, I wouldn't count the MegaUpload folks out just yet. It's probably very dependent on how much of their assets are frozen, which will affect how much of their money they can spend on legal representation. (I say unfortunately, because it seems to me that in an ideal justice system, everyone should have the same level [high!] of representation, rather than some being able to "buy" better lawyers).
In the USA at least, much of our government could function nearly the same regardless of if our market system is completely laissez-faire capitalism, or hardcore communist. In fact, you could argue that government and its' systems, like the judicial system should be completely devoid of any possibility for profit motives. Since, as saucetenuto states, those undermine the system.
Now, I don't want to get into an argument about whether good lawyers deserve to get paid better than bad lawyers, etc. But I don't think I'd want to meet the person who sees the justice inequality between rich and poor defendants and thinks "All is as it should be."
But outside of that, it's not up to the judge. It's a criminal case, and they will be tried by a jury. If they're convicted, the judge will determine their sentence. But it's not up to the judge to determine their guilt. (Unless the defendants forgo a jury trial and elect for a trial by judge, but I doubt they will.)