I don't care if the government asked for the data of one particular user, when investigating a serious crime and having probable cause. Did you read the documents you linked to? Are you saying that you don't believe that investigating authorities should ever be able to access the contents of an email account, even with probable cause?
If somebody sells me a service saying they can't provide that data, then I expect that data to not be provided. It's what I'm paying for, and it's the commitment they made to me.
Some argue that the government has no right to investigate the contents of an individual's email accounts, even with probable cause.
There's always a way to access the data. Cloud-based email is...cloud-based...which means that it's susceptible to man-in-the-middle and other forms of attack.
It's possible that the government was asking Lavabit to modify its systems such that the encrypted data guarantee would no longer be real, and then they demanded that he hide that fact.
I'm honestly not sure what to think about that. Should private data storage be permitted? Is there a difference between your private data in the cloud and your private data on a system at your home?
"Some argue that the government has no right to investigate the contents of an individual's email accounts, even with probable cause"
Who is arguing that? In this case, the issue is not about whether the government has probable cause. The issue is that any system that allows Lavabit to respond to a warrant can be used for mass surveillance, industrial espionage, etc. This conversation happened 20 years ago when people were arguing about key escrow. Almost nobody argues that the police should not be able to investigate crime; the argument is that backdoors are a massive vulnerability that leave innocent people, for whom the police have no warrant (or no "specific" warrant), at risk.
"Cloud-based email is...cloud-based...which means that it's susceptible to man-in-the-middle and other forms of attack."
The problem is not that the mail service is run by a third party. The problem is that encryption, decryption, key storage, and even key generation are being performed by a third party. I send encrypted mail through GMail all the time -- and Google is not able to decrypt those messages, even if they are presented with a warrant. While it may be problematic for the police to face such a situation, it would be problematic for me if criminals and spies could read my emails, and at the end of the crypto wars Congress determined that the need for good civilian crpytography vastly outweighed the government's needs to enforce laws and spy on other countries.
It is also important to remember that the police can still get messages that are encrypted/decrypted offline, they just have to work a bit harder for it. For example: