No one designs systems like that because, up until now, the threat of having the feds confiscate your private SSL keys was unthinkable for those of us who don't wear tinfoil hats.
And it's still not 100% clear that forcing a business to hand over their keys is even legal from a constitutional standpoint.
The site wasn't designed to be 100% secure most likely due to it being overly complex and burdensome on the end user, thus reducing uptake. So a comprise was made and that is why it was designed the way it was...thus leading to a subpoena for the entire site since Lavabit didn't comply with handing over a specific users data.
Also it is legal for the site to hand over their keys, it already happened. The only way it will become illegal is if the law somehow gets repealed.
What? The site WAS designed to be 100% secure, which is why the government demanded he hand over his private keys.
There was no compromise anywhere, financial institutions use the same exact security strategy. An insecure system would be one that makes it easy for a 3rd party to intercept communications (via warrant or through a disgruntled employee or whatever), that is basically what you are suggesting.
And it's still not 100% clear that forcing a business to hand over their keys is even legal from a constitutional standpoint.