"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.