The term "Plan B" hits the nail on the head. John is definitely a caluclating type who planned ahead here.I agree entirely. I really don't think John thought their staging would fool anyone for a long period of time so he created a Plan B for himself.
He knew the staging was poor and when he had brought up JonBenet's body from the basement and looked in L. Arndt's eyes, he waited for the axe to fall. Arndt caught the terror in John's eyes, and became afraid he would attack her. But I think it was plain fear in his face. He expected them to be arrested on the spot.
They should have done that, or at least have taken them to the police station at once for separate questioning. The police would also have had the legal right to collect their clothes immeditaley.