The story is the FBI asked for Snowden's emails and correspondence. Lavabit said they would not hand over the information(but admitted they had the technical capability ... it was server side encryption after all). Only after that refusal did the FBI start taking more drastic action.
This is, if that story is true, about on par with a Bank complaining that the FBI ransacked the safe all their safety deposit boxes were stored in. Expect the bank neglects to mention that the only reason the FBI had to break open the safe and be put in the position of being able easily break open all the safety deposit boxes was because the Bank failed to to hand over one box when given a valid court order.
This is particularly problematic in Lavabit's case because a major cornerstone of the argument against the NSA's warrantless surveillance is that there are legal means to compel access to data when it is actually necessary and that those means make it totally illegal to do what the NSA was doing. This is really a hard point to argue when those means don't work because other's thumb their nose at the law as well.
[0] http://www.wired.com/threatlevel/2013/10/lavabit_unsealed/