While you may not think much of the distinction, it wasn't the FBI that decided to shut them down - it was the judge that decided there was probable cause and thus signed the seizure warrants. So the judicial branch made the decision - this is the same branch that can imprison you before you're found guilty if they believe you're dangerous or a flight risk.
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.
I think the reasoning the feds use is it prevents the suspect from destroying evidence, and/or stops the activity from continuing to 'harm' the public.
But then they better have damn solid evidence first that the additional time period the company is left operating will be instrumental in increasing the damage done sufficiently to make significant difference. In this case Megaupload have been operating for years.
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.