This reminds me of an idea I had a while back, the POD is slightly different but the end result is more or less the same as the OP.
Basically, my idea revolved around having a "Great Man" arise from among the tribes in the Indian Territory prior to the American Civil War. One of the possible candidates I was considering was a surviving Lyncoya Jackson. Anyways in my TL, Lyncoya Jackson manages to convince the tribal leadership of the Indian Territory to form a coherent form of government in order to best handle the upcoming conflict between the North and the South.
With the secession of South Carolina, the Tribal Council begins to debate whether or not to secede or remain in the Union. Eventually a third option is settled upon and as soon as the outbreak of hostilities occur, Lyncoya Jackson leads the residents of the Indian territory in a relatively bloodless insurrection seizing all US forts and positions in the region and sending their garrisons back to their respective states. Diplomats are then sent to both the nascent Confederacy and the Union in order to secure the best possible deal for the Indian territory.
Though both the US and CS governments consider re-conquering the rebellious Indian Territory, neither eventually opt to do so due to the expanding nature of the civil war. As the war drags on, Lincoln sees an opportunity in the Indian territory situation to demonstrate his willingness to negotiate and bring about a quicker diplomatic end to the American Civil War. To this end the Indian territory is offered an incredible deal, which includes statehood and considerable internal autonomy including the retention of slavery should they choose to join the Union and contribute forces to the suppression of the rebellion. A lack of similar counter-offers from the CSA lead the Tribal Council to accept the offer and the treaty narrowly passes through Congress.
Though the successful negotiations with the Indian Territory fail to bring about a significantly earlier end to the American Civil War, the participation of Native cavalry in the conflict significantly influence events in the Trans Mississippi theater resulting in an earlier capture of Vicksburg and an earlier end to the War. Thus following the end of the war the Indian Territory finally ratifies it's constitution and is admitted into the Union.