Overall the EO stands. In hindsight, they should have been clearer about those in transit. But, that said, the judge should have left things alone to be worked out. These were political decisions. Since when, anyway, do non-citizens get habeous corpus rights to enter the US. It is clear, and Obama's actions gave clarity, that it is the executive and government that control immigration. Not the courts, not the states, not counties, not cities, and not the media.
these people that started legal action were pre-planned with lawyers waiting for them at JFK. This was not accidental.