And yes, I understand how wrong this can be. Seizing a website, shutting down an entire corporation, is a huge thing that can't be done lightly. Just like accusing a man of child pornography and seizing every electronic storage device he has can't be done lightly. In both cases you destroy something.
So yes, this power can be used very, very wrongly. But in this case it was not. The Feds did their homework. MegaUpload was a corporation very blatantly, flagrantly and proudly existing solely to transmit pirated materials.