According to W. D. Fenton, President of the Oregon Historical Society, Lee held the one mission officially and the other in secret:
While his first and dominating purpose was the work of the mission, he saw at once the possibilities of government and its close relation to the cause in which he was ostensibly and directly engaged. He prepared a petition and forwarded the same to Congress, and Caleb Cushing, of Massachusetts, requested further information from him. Lee had returned to New England, and on January 17, 1839, wrote from Middletown, Conn., that there were in Oregon, belonging to the Methodist mission, 25 persons of all ages and both sexes who would shortly be reinforced by 45 others, making 70. ....
The memorial drawn up before Lee left Oregon was presented to the Senate by Linn of Missouri, on January 28, 1839, and on December 11, 1838, Linn, as you will recall, had introduced a bill in the Senate for the occupation of the Columbia, or Oregon River, and to organize a territory north of 42 degrees and west of the Rocky Mountains to be called Oregon Territory. This measure also provided for the establishment of a port of entry, and the extension of the revenue laws of the United States over the country. Senator Linn followed this formal action on his part by a speech on the 22nd of February, 1839, supporting a bill to provide for the protection of of citizens of the United States then in the Territory of Oregon or trading on the Columbia River. It is a matter of history that Jason Lee was the unseen hand behind this first active effort at Washington, and he was regarded in a special sense as the non-commissioned representative of the Government of the United States.
At this time an appropriation of considerable money from the secret service fund of the United States was made for the charter of the ship Lausanne. This was known only to Jason Lee, and was not revealed or disclosed until the boundary question was settled between the United States and Great Britain by the Ashburton treaty of June 15, 1846. 
He died retaining this secret to his death, which only history and time revealed.
Sixty-one years passed and the recount of his alleged infidelity to the Christian mission did not keep by those who spoke of him. He was seen instead as a hero for both purposes. How would we think of this kind of missionary by today's standards?
1. Lee, Jason. "Memorial Services at Re-internment of Remains of Rev. Jason Lee." Salem: Salem Public Library, 1906; pg. 12.