How about being innocent unless proved guilty? Megaupload went down without any trial, and even though the site was obviously used for piracy (was it really?), that should still be proven in court and then only the illegal section of the website should be removed from web.
There's really nothing unique about that. If you were accused of selling drugs via a restaurant front, it'd be shutdown while you're standing trial too.
There is no general authority for the police to abruptly shut down a business. Once a warrant has been executed, the police leave and the business can reopen at its leisure, even if it might need to replace some equipment and staff.
The authority given to courts and federal authorities to behave as they are for suspected copyright infringement is extremely abnormal and cause for great consternation as to the direction of our legal system.