There is no final court order yet, there is a temporary stay and this order merely prohibits deportation, not the detention or turning away of immigrants coming in. This order is just one small step in what is going to be a long hard case.
It'll probably end up going to the Supreme court, the Supreme court has two Obama appointees and with justice Scalia passed away there is a chance it could go in the ACLU's favor. . . but established constitutional law is clear, the Supreme court has ruled time and time again that America can turn away anyone at the boarder and non-citizens do not have a right to stay in America . . . so defeating this executive order at the Supreme court level will require some doing, which might happen because of the current composition of the court has judges that are willing to veer away from established precedent.
It's not even given Trump's admin would actually defend the position of turning away green card holders. So far there was only emergency stay which AFAIK does not even require participation from the other side, so we have no idea what position or argument the administration has on the case. The judge (quite correctly) decided to issue an order that causes least harm (not deporting anyone, but not ruling any broader) so I think we'd know on Monday more about admin's position on this.
ACLU of course would argue the whole order is invalid, but I don't think this part would be easy to prove and not likely to get emergency order broad enough, and it probably would take more than 60 days to go through which means challenging this particular order in its entirety may be moot by the time it gets to any sort of trial. If the subsequent policy will match it though it still may have a point.
> Stephen Miller, a senior adviser to the White House, said: "Nothing in the Brooklyn judge's order in anyway impedes or prevents the implementation of the president's executive order which remains in full, complete and total effect."
It'll probably end up going to the Supreme court, the Supreme court has two Obama appointees and with justice Scalia passed away there is a chance it could go in the ACLU's favor. . . but established constitutional law is clear, the Supreme court has ruled time and time again that America can turn away anyone at the boarder and non-citizens do not have a right to stay in America . . . so defeating this executive order at the Supreme court level will require some doing, which might happen because of the current composition of the court has judges that are willing to veer away from established precedent.