"No employee of the executive branch acting in their official capacity may advance an interpretation of the law as the position of the United States that contravenes the President or the Attorney General’s opinion on a matter of law"
Any employee obeying a SCOTUS ruling is in violation of this EO, unless the President agrees to that ruling.
No EO may say that SCOTUS can override them, but no other EO blocks federal employees from obeying SCOTUS.
"Any employee obeying a SCOTUS ruling is in violation of this EO, unless the President agrees to that ruling."
You forget the entire framework for EOs. No EO has "except when a court says otherwise". The EOs are subject to checks and balances, such as judicial review. If the EO exceeds its authority (not based on congressional or constitutional means) then it won't be valid. Meaning you can't grant yourself powers that you don't have the authority to grant under the framework. There's case law you can go look at for a history on it.