I am not a UK citizen so I can't say with any level of certainty what the process was designed to be. However, a few things seem pretty obvious. 1) The judges said this was "inconsistent with EU law". That means it is illegal because it goes against the (higher) EU law. This is equivalent to how Federal law trumps State laws in the US and State law trumps local/municipal law. If it is inconsistent with EU law, then it is a violation of that law, plain and simple. 2) The judges also held the ruling in #1 based on lack of "prior review by a court or independent administrative authority". That's the US equivalent to what we call due process. So rights were being violated without due process. That's pretty serious.

I think you are making the water murkier by trying to imagine what you think the process is/should be. The fact remains that the law has been violated on a mass scale, by government, and this has now been adjudicated in a court of law.

What is happening is that the court has decided law X is not consistent with law Y.

In the UK system, when this happens the courts can order Parliament to review law X to make amendments so the laws are consistent. The Government can choose to appeal this to a higher court or they can choose to amend the law. (Incidentally this differs from the US system in that the court doesn't say what the new law should be - but rather says that a section of the law is invalid in a certain way and must be changed - a job then left to the politicians).

No law has been disobeyed at all here - rather two perfectly valid laws have been created that are in disagreement, and the court is ordering that the disagreement be resolved in favour of one.