It would be more accurate to say that prior to this ruling, any of 700 district judges could unilaterally block the president from exceeding his authority under the constitution pending a review, including matters of national security, based on their own subjective view of the law. It may differ in other countries, but under the US Constitution, the judicial branch ultimately decides the limits of executive authority, not the President.
If it's truly a matter of national security, the President could always file emergency appeal and it would almost certainly be granted. If it's such a dire and immediate emergency that even those few hours were critical, it's doubtful that any President would feel obligated to obey the injunction anyway.
Far from preventing the proper functioning of government, this was one of the few remaining guardrails maintaining the proper functioning of government under unprecedented circumstances.