Well, there is a general principle that police can do things that ordinary citizens cannot. But, subject to rules, not indiscriminately. For instance, they can enter a property if they have a warrant, whereas if someone else does this, it is break and enter. If the FBI established "probable cause" that the server is used for crime, they could have gotten a warrant. I can't imagine it would have been difficult, so why wouldn't they have taken the legal precaution.