When Madame Fraunces had been killed with blood spilt on the floor, Calhoun knew that Morganna would not leave it at it. The Queen wouldn't be satisfied with just the death of the woman who was close to Theodore, she would go to great lengths to frame Theodore and him, taking advantage of the situation.
Every step that Morganna took, she didn't realize she was making way for Calhoun and he was making use of her for his own benefit.
The day when Madame Fraunces was found dead, Calhoun had not only moved the body where the royal family would least suspect, but he had gone back to the house at the same night to replace the wooden planks before he had spilt juice that was extracted from beetroot. This gave an effect of blood before he left the house.
The Queen acted just as he had expected, tipping the magistrate as well as the guards to drag Theodore to be executed, but she wouldn't have guessed that the High House would be on her trail now.