I do remember that being a scandal.
To your main point, a story has been going around that a court has put a stay on the executive order. If true, this would mean that enforcing the order is currently illegal; and doing so could be called a "coup" by the executive branch (although I don't think this technically qualifies as a coup).
Having said that, my understanding is that the referenced court case only applies to the specific individuals who sued, so enforcement of the order is still legal in all other cases.
I understand the DHS statement to simply amount to "we aren't lawyers, so until a judge rules on whether the entire order is constitutional, we have to assume it is and act accordingly. We have lawyers on staff who will tell us how other rulings affect our actions, and how far those rulings go."
It's important to remember that executive orders are legally binding on people who work for the president, but not anyone else. Usually, they say how an ambiguous law will be interpreted, or they add limitations on top of what the law requires.
In this case, the president has directed various people to take certain actions. The courts will have to determine if those actions are legal. It wouldn't surprise me if some actions are legal (cabinet members are supposed to review the policies for the refugee program) and others aren't (prioritize immigrants based on their religion). But DHS doesn't get to conduct its own review of the order; they have to assume the whole thing is legally binding.
If multiple federal courts start granting injunctions against particular parts of the order, then things might change. I'm not sure how that works; although I am sure that government-paid lawyers will conduct their own review of the order, and I strongly suspect that the president has to approve any decisions to not implement a portion of an executive order.
Maybe you can link me to the comment thread where HN was breathless about the need for assassination or civil war.
That story is false (at least as far as I know). The stay was put on one detail of the implementation of the order, not the whole order - namely, on deporting green card holders that has already arrived in US airports.
See: https://en.wikipedia.org/wiki/Darweesh_v._Trump
> Having said that, my understanding is that the referenced court case only applies to the specific individuals who sued
ACLU is seeking class action status, but in the meantime if several judges agreed that the stay is warranted I imagine it would be not hard for any person (with access to law assistance etc. of course) to be able to obtain similar order.
That sounds for all the world like the executive branch rejecting the authority of the judicial branch.
The statement then goes on to say:
"The Department of Homeland Security will comply with judicial orders..."
So no, the executive branch is not rejecting the authority of the judicial branch.