If I was in their shoes, I would grab the whole rack of servers too since there must be some golden nuggets hidden inside most servers. But it is bad to bring down sites that are not part of the initial investigation.
The F.B.I. seized an entire rack Web servers in a raid on a data center. Several Web sites, including those run by the New York publisher Curbed Network, went offline.
"DigitalOne provided all necessary information to pinpoint the servers for a specific I.P. address, Mr. Ostroumow said. However, the agents took entire server racks, perhaps because they mistakenly thought that “one enclosure is = to one server,” he said in an e-mail."
The raid also affected a server used by Instapaper, a popular service that saves articles for later reading.
Pinboard, a bookmarking site reports "We have three big servers with one hosting company (DigitalOne). Two of them are online, but our main database server is unreachable. Basically it is cut off from the world because of network problems at our provider."
F.B.I. Seizes Web Servers, Knocking Sites Offline - NYTimes.com
The article didn't say what they were looking for, but I recently read that there are 1.5 million hack attempts on the Pentagon servers every year and they are they are going to start going after the hackers aggressively. The server that they want is probably either part of that sweep or related to a terrorist organization. It is too bad that they had to take down several unrelated sites in the process.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin
Just goes to show that you need to have a backup copy of your site. If the site goes down and you have a backup, then you should be able to easily restore it elsewhere on a new server at another web host.
One in four US hackers 'is an FBI informer
The FBI and US secret service have used the threat of prison to create an army of informers among online criminals
"In some cases, popular illegal forums used by cyber criminals as marketplaces for stolen identities and credit card numbers have been run by hacker turncoats acting as FBI moles."
One in four US hackers 'is an FBI informer' | Technology | The Guardian
bogart (29 June, 2011)