If you're hosting encrypted data that focuses on privacy while remaining law abiding, it's just sensible to maintain separate SSL keys so you avoid this very scenario. It's not as if it wasn't foreseeable.
If you have separate server certs per user (as suggested above), then you can tell which user is using the service.
If you have separate client certs per user, then you call tell which user is using the service.
The Lavabit response to the original order was not the best, IMHO. As he was in possession of the certs and private keys, he could have decrypted Snowdon's traffic himself, and handed it to the court.
Instead, he tried to hide behind a BS "it's encrypted" defence. The court called his bluff. He lost.
I would imagine him decrypting the data himself would cause problems in a chain-of-evidence type of way though.
Anyway, at least in the physical security industry, security isn't about preventing intrusions. It is about delaying it and limiting it until a sufficient response can be mobilized. Perfect security is impossible
How the guy chose to run his business and what the warrant was requesting are two different things.
Yes a warrant imposes certain restrictions on your business.
What you are describing does happen, but I fail to see how it would happen under a search warrant.
As for your destroying data being against the law if it is requested by the courts. You are correct, except that if your business model is to destroy data in a timely manner then you cannot be held in contempt for destroying data before it was requested. At that point it becomes something different as they have to request you no longer destroy that data so that they can collect it. I don't see how that request falls under a search warrant. I suppose it could happen if a judge likes being overly broad in search warrants (which could cause problems in the criminal case), but it seems unlikely that's how a typical search warrant would be executed.