While I cannot address all Native American nations at this time, the threat of attacks from multiple nations, or even a united pan-Indian uprising, was very much a concern for white settlers from Minnesota to Colorado and New Mexico during the Civil War. I will modify an earlier answer I gave here to address your question. As you will see, an atmosphere of fear and paranoia permeated much of the West, leading to horrendous acts of violence during the Civil War.

By way of background, the 1851 Treaty of Fort Laramie between the United States and the Cheyenne, Sioux, Arapaho, Crow, Assiniboine, Mandan, Hidatsa, and Arikara set aside the land between the Heart River in North Dakota and the North Platte River in Nebraska from the Rockies to western Kansas as Indian territory. The discovery of Colorado gold in 1858, and the unprecedented influx of European migrants violating Cheyenne and Arapaho territorial claims, prompted the contentious Treaty of Fort Wise in 1861 that diminished reservation land by over ninety percent. Many influential Cheyenne and Arapaho refused to uphold this second treaty signed by such a small minority of leaders, which was contrary to normal deliberations within the community. Colorado authorities chose to interpret this dissension as prelude to war.

After the 1862 “Great Sioux Uprising” in Minnesota a shroud of fear engulfed Colorado Territory. Fear only multiplied in 1863 with the transfer of troops east to Missouri to help with the war effort. Rumors abounded, stating the Cheyenne and Arapaho would seize the opportunity to retaliate, or Confederate agents were rallying Plains nations to rise against white settlements. Colorado authorities actively fanned the flames of panic. During his testimony before a congressional investigating committee Kit Carson stated “the authorities in Colorado, expecting that their troops would be sent to the Potomac, determined to get up an Indian war” (quoted from Calloway, Our Hearts Fell to the Ground). In April 1864, Colorado soldiers started attacking a number of Cheyenne camps, and in May Lieutenant George S. Eayre encountered a Cheyenne buffalo hunting camp near the Smoky Hill River. Lean Bear, who a year previously visited Washington as part of a peace delegation, approached Lieutenant Eayre’s troops “intending to show his papers and shake hands.” The commander ordered his men to open fire, “then the troops shot Lean Bear to pieces, as he lay on his back on the ground” (Bent, quoted in Kelman A Misplaced Massacre).

In this volatile atmosphere, any aggression, any raid, any theft was interpreted as the first volley of an uprising. In June 1864 four Arapahos killed a white family near Denver. With the murdered family on display in Denver “Governor Evans issued a proclamation advising ‘friendly Indians’ who wished to avoid being mistaken for hostiles to place themselves under the protection of the military at Fort Lyon” (Calloway Our Hearts Fell to the Ground). Believing the promise of peace in a dangerous time Southern Cheyennes Black Kettle and White Antelope, as well as Left Hand of the Southern Arapaho, relocated women, children, and elders to the fort. Most adult males failed to make the trip, choosing to continue hunting to boost winter stores before the snows fell.

Colonel John Chivington, commander of the Third Colorado Cavalry, a Methodist preacher, an opponent of slavery, and man who stated “I have come to kill Indians, and believe it is right and honorable to use any means under God’s heaven to kill Indians” arrived at Fort Lyon. Into this toxic atmosphere of fear he combined forces with the First Colorado Cavalry and rode toward Sand Creek. Before dawn on November 29 Colonel Chivington ordered a coordinated attack against the village. Only two officers refused the order.

George Bent, a half-Cheyenne residing in Sand Creek, stated

I looked toward the chief’s lodge and saw that Black Kettle had a large American flag tied to the end of a long lodgepole and was standing in front of his lodge, holding the pole, with the flag fluttering in the grey light of the winter dawn. I heard him call to the people not to be afraid, that the soldiers would not hurt them; then the troops opened fire from two sides of the camps. (quoted from Our Hearts Fell to the Ground)

Bent later asked his friend Little Bear to recount his experience of that day.

I ran to our lodge to get my bow, quiver, shield, and war bonnet. My father, Bear Tongue, had just recently given me those things. I was very young then and had just become a warrior.

By this time the soldiers were shooting into the camp from two sides, and as I put on my war bonnet and took up my shield and weapons, the bullets were hitting the lodge cover with heavy thumps like big hailstones… The people were all running up the creek; the soldiers sat on their horses, lined up on both banks and firing into the camps, but they soon saw that the lodges were now nearly empty, so they began to advance up the creek, firing on the fleeing people…

I passed many women and children, dead and dying, lying in the creek bed. The soldiers had not scalped them yet, as they were busy chasing those that were yet alive. After the fight, I came back down the creek and saw these dead bodies all cut up, and even the wounded scalped and slashed… I ran up the creek about two miles and came to the place where a large party of the people had taken refuge in holes dug in the sand up against the sides of the high banks. I stayed here until the soldiers withdrew. They were on both banks, firing down on us, but not many of us were killed. All who failed to reach these pits in the sand were shot down. (Little Bear, quoted in Calloway Our Hearts Fell to the Ground)

In 1999, archaeologists identified the site of the massacre when they unearthed 12-pounder cannonballs, the type used by Colorado Cavalry, and “the only time artillery was used against Native Americans in eastern Colorado” (Smiley). Distribution of bullets and projectile points verified Cheyenne and Arapaho oral history of the encounter, and indicated to the field director Doug Scott “there was very little evidence of defensive fighting in and around the camp, supporting the concept that this was a surprise attack and was, indeed, a massacre” (quoted in Smiley). Roughly 270 Cheyenne and Arapaho perished at Sand Creek. White Antelope died in the attack, and trophies stripped from the dead, including body parts, were displayed throughout Denver. As word of Sand Creek spread the Indian War white settlers feared, and actively instigated, spread across the Plains. Black Kettle survived, and was later killed in Custer’s attack on his village on the Washita River four years later.

Sand Creek was not the only violent encounter between the United States and Native American nations during the Civil War. In Minnesota, the years preceding the war left the Sioux deeply malnourished. Chief Taoyateduta/Little Crow attempted a decade of accommodation, trusting the exchange of land for annuities would be upheld by the United States. Oral tradition states when Taoyateduta/Little Crow informed an Indian agent his people were starving the agent told them to eat grass. Unable to control the anger and frustration boiling over within his community, Taoyateduta/Little Crow unsuccessfully tried to warn against violence. In the “Great Sioux Uprising” that followed roughly one thousand white settlers were killed. After a few initial victories the tide quickly turned and the Dakota were defeated. 1,700 survivors were marched to Fort Snelling. Four hundred were tried and thirty-eight executed in the largest public hanging in American history. In 1863 Colonel Patrick Connor and California Volunteers attacked a Shoshoni-Bannock village on the Bear River, killing more than two hundred men, women, and children. In the Southwest hostilities against the Navajo culminated in a 400-mile forced relocation, the “Long Walk”, to the Bosque Redondo Reservation. More than two hundred died en route, followed by more than two thousand who perished during their imprisonment due to malnutrition, disease, drought, bad water, and rations unfit for human consumption (Calloway First Peoples).

The Civil War only increased the simmering fear of Native American resistance and served to fan the flames of violence across the West. Violence and intentional resource deprivation would continue for several more decades as the United States sought to open land to white settlement and confine Native Americans onto reservations.

In a word, no, none of the so called Five Civilized Tribes in Indian Territory (now Oklahoma) tried to throw off both Union and Confederate government control or try to take back their land. This is what happened.

Before the Civil War started, the Union withdrew all of it's troops from Indian Territory and abandoned it's forts therein. Confederate troops then occupied those forts. Confederate raids were launched from Arkansas into Indian Territory. The only organized military power in Indian Territory was Confederate.

Then the Confederacy offered each Tribe an alliance in which the Tribes retained their tribal boundaries and the Confederacy agreed to protect those boundaries. However the tribes would remain under some sort of control by the Confederate government. The Confederate alliances were more benevolent and protective than what the Five Tribes had seen from the Union.

So each tribe divided internally between a Confederate faction and a Union faction. Many union supporters fled north to Kansas because the land was basically under Confederate occupation, and the remaining Confederate supporters of each Tribe (although not a majority of the entire tribal council) signed alliances with the Confederacy.

Trivia items: Jefferson Davis was posted to Ft. Gibson (the most important fort in Indian Territory) during his service in the American military. Cherokee Stand Watie was the last Confederate general to surrender on June 25, 1865, at Fort Towson in the Choctaw Nation.