Every rule & regulation creates winners and losers.
We want the legislature to pass laws that create net positive effects - the benefits should be larger than the costs.
Some laws spread costs and benefits pretty evenly - no compensation is needed for those. But others concentrate costs on a few, for the benefit of the public at large. In those cases compensation for the losers seems only fair.
If you can't afford to pay the compensation, that's a sign that you've got a bad law - the benefits are supposed to be bigger than the costs.
The result here is a shame, but I don't blame the court too much. Lavabit screwed up big time.
Anyone running a service whose operation is likely to frustrate the authorities (even if that's not the intent, and legal and legitimate as it may be) needs to have good legal help a single phone call away from day 1.
If you don't have that, you're not serious about it.