But it's not madness based on the intended structure of government? The EO isn't saying "ignore Constitutional violations". It wouldn't be valid if it did.
If Congress passes a law that say "tobacco is banned", and the US President says "I will direct my agencies to follow this new law" and you have agencies saying "I'm not a lawyer, but I feel like this law is unconstitutional so my agency is not going to follow it!"?
How would the government even function if you have 100 agencies with 50 of them having the power to come up with their own interpretation of the law? How is that even workable as a branch of government?
The executive branch of government is more accurately viewed as a monolithic organization which derives 100% of it's authority by delegation from the US President. This is why the president personally selects the heads of each agency (with the Senate approving). Authority moves down from the president all the way to the most junior government employee - they are acting on behalf of the president.
> There will be disagreements within a branch that will need to be worked out.
What does "worked out" mean?
For legal issues the President will consult the US attorney general. If it's complex, the DOJ might create a white paper determining the constitutionality of a law or not.
To have an agency head disagree with that determination seems like a rogue agency. Why would that agency head know better than the attorney general?