God knew that Adam and Eve had to have somehing of the Knowledge of Good and Evil before they could sin. No one had to tell God, it was part of the plan for creation. 

Primacy of conscience does not mean people cannot be punished for crimes others judge that they have committed, it only means God does not hold them as culpable as someone who does know. The Nazi soldier can be condemned even though he follows his conscience. Jesus was condemned to death even though he followed his conscience. People  judge by appearances, God looks at the heart. See 1 Sam 16