Complex sentence: Broyles, having listened to Olivia's conversation, knows that she has broken her conditioning, as the FBI had ceased to exist decades earlier in the parallel universe, but because of her efforts to save Christopher, he lets her go.
Split into simpler sentences: Broyles, having listened to Olivia's conversation, knows that she has broken her conditioning, as the FBI had ceased to exist years earlier in the parallel universe. Because of her efforts to save Christopher, he lets her go.