It's not about free speech
The judge in the case says that what the FBI wants the courts to order is illegal; the District Court's decision says in part (on page 30) :
"I therefore reject the government's interpretation of the AWA's gap-filling function, and conclude that a judicial order that would confer authority that Congress has considered and decided not to enact is not "agreeable to the usages and principles of law."
See https://www.eff.org/files/2016/02/29/applebrooklyn-2.29.16order.pdf