Just like darkness is another part of light, and therefore darkness can not stand before the light, but it stands somewhere by the side of the light. Without light, there is no existence of darkness, but darkness cannot be found in the light. Similarly, there is no darkness or activities of the external energy in the Pastimes of Lord Caitanya.
So far as Acyutananda and Jaya Govinda are concerned, I am not displeased with any of my disciples. A father can not be displeased with his sons, but sometimes the sons create disturbances, and the father has to tolerate. Constitutionally, the father is always affectionate and pleased with the sons. But it is up to the sons to obey the father and keep the relationship natural. The little disturbances created by Acyutananda and Jaya Govinda were temporary. Now again they have come to their real consciousness.
Regarding your question about Subhadra and Durga, they are not at all the same. Durga's other name is Bhadra, not Subhadra, and Durga's activities are within the material world. Subhadra does not work as Durga. Subhadra is internal energy, and Durga is external energy. As energy, they have a relationship as much as we are energies of Krishna, but the energies are working in different capacities. Although originally the energy is one, by their expansion, the accents of the energies are different, and as we are not impersonalists, this variegatedness of actions are essential for the Supreme Personality of Godhead, as much as the government is one but there are multi-departments for management of the government. The education department and the criminal department are all departments of the government. The government is connected with all parts and departments, but the education activities are different from the criminal activities. This is the philosophy of inconceivably simultaneously one and different manifestations of the Absolute Truth.