It is interesting that the prosecutor portrayed this as a pen trap. Courts have ruled that users do not have a reasonable expectation that the numbers they dial on their phone line will remain private (basicaly because they show up on the bill) but that they do have a reasonable expectation that nobody is listening in. That is why this information can be obtained without probable cause. But if Lavabit offered specific guarantees that this information would not be recorded except in the encryted e-mail boxes, then the users had a reasonable expectation of privacy. This might make the use of a pen trap without probable cause illegal.
A private contract between a company and end user does not increase a right to privacy with respect to the government. In this instance it _might_ have triggered a lawsuit by users against Lavabit for breach of contract. Lavabit would win such a suit with the defense of having followed a court order.