Again, this is not the servers breaking down in a freak accident. This is the feds making a conscious choice to shutter service regardless of legal users, with servers and an infrastructure already there to provide said users to reclaim what they put up.
How do the police do that in this case?
Imagine a storage facility the size of texas, where millions of people go in and out of the gates daily, and it stores billions of their items.
Not only do the police find out that criminals are using the facility, but those who own and operate the facility work with the criminals - paying them off, giving them special treatment, and making money by charging each person who goes through the gates to visit the criminals.
The owners are running an enterprise that not only facilitates criminal activity, but they are profiting off it, and altering their services to make it easier for the criminals. They are acting as brokers between the criminals and their clients, and skimming a bit off each "sale".
The police recognize that there are millions of legitimate users. But there is simply no way to leave the facility open without also leaving most of the criminal activity intact. They can't staff enough guards to manage millions of people trafficking in items each day.
Further, the business is so highly technical and secure that they don't even have a chance of keeping it up and running without the help of the criminals who run it. At best some user might be able to get some data, but that's not even likely if the owners don't give them information on running the place.
We could extend the dry cleaner analogy similarly - the ticket system is contained on an encrypted computer, and there are billions of clothes hung up, each with a number. Without the owner's help, there's no way for the police to get into the computer and figure out who owns what, and that doesn't even account for the fact that well over half the clothes in the cleaners were obtained fraudulently, so they have to also figure out who is a real customer, and who is criminal as people come by to pick up their stuff.
The only solution is to not prosecute them, which is I guess what you're arguing for. Or to give them advance notice. "hey, we're taking you guy down next week, please notify your customers - but not the criminals - that they need to get their stuff off now."
I think you're expectations are off base and unrealistic.