"They ask: If court orders are legitimate, why should we allow engineers to design services that protect users against court-ordered access?"
Why on earth would you allow that a court order is legitimate? Both the tactic and the execution are of questionable legality, and critically that legality is flexible.
Remember that the clearly illegal complicit acts of telecommunication companies were made retroactively legal through a grant of immunity. The idea that you would begin your article by allowing the emperor to retain the assumption of clothes undermines the credibility of your remaining contentions. Courts having the right to demand things from citizens that they do not wish to divulge is not some force of nature, it has not always existed, does not exist in all systems, and need not exist in the way it currently does.
So cut the crap trying to justify the moral, conscientious, and brave action of a small company and force them to justify their existence.