He was not an "agent" in the sense of an "Indian Agent" appointed by the Indian Office. He was acting as an agent to sell cotton and purchase supplies under the authority of Gen Kirby Smith, perhaps at the request of the Choctaw Nation.

Unless there is other correspondence I'm not aware of, I didn't get the idea that Bourland (Whaley) was suggesting anything suspicious about his papers. I thought he was merely stating that he had performed a proper review of his papers, as he would do with anyone, and found them to be in order. Perhaps his point was that he and other officers were prohibited from interfering with his business because of Smith's authority. Any officer might confiscate any goods or money at any time as they saw fit for "the cause", particularly from the Indian Nations -- the chronic problem of Pike and repeated complaint of the Indian Nations -- and it required orders from Smith to prevent that from happening again.