In a period of federal expansion, pre-existing governments presented a problem for those who were inspired by manifest destiny. Therefore tribes had to be re-defined as a collection of individual wards of the state, rather than self-governing nations. In contrast, tribal sovereignty was more consistent with the Confederacy's views on States' rights (as long as you weren't a Cherokee living in the middle of Georgia, thanks to Andrew Jackson) but more practically, the recognition of tribal governmental power was a method of cementing an alliance on the sparsely populated but chaotic frontier.
Albert Pike, the man responsible for the success of the Confederate efforts to gain alliances with the Five Civilized Tribes, was fully devoted to the betterment of the South's Indian wards. In August, 1862, he forwarded an eleven-point program to President Jefferson Davis designed to carry forward the good relations which had been established with the Indians. (p21)
The treatment of the Indian troops and the supply system of the Confederate army also was discussed. Pike advocated the immediate dismissal of any officer who seized supplies en route to Indian Territory, and the direct shipment of all monies allocated to the Indians to the officials responsible for their distribution. ...Pike likewise prodded the Confederacy to honor claims for supplies which had already been provided by the Indians. (p22)
Thus the man who had done the most to gain Southern treaties with the Five Civilized Tribes proposed a program which was designed to ensure the success of the relationship. Just how much the Confederacy was to ignore Pike's advice can be seen in the early attempts at implementing the treaty stipulations. Though the programs outlined for Indian Territory were well organized and developed, they never were adequately initiated and maintained. All of the agreements called for the furnishing of Indian troops for the protection of Indian Territory. These troops were to be used exclusively with in the boundaries of Indian Territory and were not to be subject to service elsewhere.
The number of men to be raised varied among the tribes. The Creeks and Seminoles pledged a regiment of 10 companies; the Chickasaws and Choctaws were to furnish one regiment. The Cherokees not only agreed to the raising of one regiment, but also to the furnishing of two reserve companies. All of these troops were to be mounted, and their officers were to be elected from among the troops. The Confederacy was to assume the burden of equipping and paying the forces. These Indian troops were to be graded the same pay and allowances as all other Confederate forces. (p23)
The Confederacy next began to assimilate these forces into its military structure. The first military command of the Indian Territory was created on May 13, 1861, when Brigadier General Ben McCulloch was given the command of the district of Indian Territory... The nearly unanimous decision of the Federal Indian agents within Indian Territory to side with the Confederacy gave the self a nucleus on which to build inefficient agency system among the Five Civilized Tribes. (p24)
The Confederacy, by its own bureaucratic blundering and ineptness, failed to formulate a clear and concise program needed for the success of its efforts and Indian Territory. Had the South followed the suggestions of Pike's proposals, perhaps the confusion resulting from the attempts at creating an Indian policy would have been avoided. (p26)
Of all the civil functions promised in the Indian treaties, the one calling for the creation of a court system within Indian Territory was probably most widely hailed by the Indians. Because they had long experienced white man's laws as applied to the Indians on white man's ground, they were eager to have control over their own judicial system. ... These courts were to be regular district courts of the Confederacy with the exclusive power in criminal cases to try, condemned, and punish offenders who violated the law. They also were empowered to pronounce sentence and carryout execution. They were to exercise the same judicial power as any other district court system in the Confederacy. (p28)
The judiciary was given the full faith and credit of the judicial officers of the same grade and jurisdiction in any of the Confederate states. Thus was established for Indian Territory a workable judicial system based on the same rights and privileges as white citizens of the Confederacy, and on equal terms with other Southern states court systems.
... Extradition was provided not only among the Indian nations themselves, but also between the Indians and the other states of the Confederacy. These actions by the South of virtually ended all discrimination based on the Indian blood within the Confederate court system. ... Like the other civil services which the South attempted to establish inside Indian Territory, this one also failed.
... This inability of the Confederacy to fulfill his obligations to the Indians was blamed on the disturbed condition of the country. Whatever the reason, the question of the courts remained a course of dissatisfaction among the Indians throughout the war. ... The Indians were allowed to tax all licensed white traders of importing goods into Indian Territory. (p29)
To permit the Indians to participate fully in the government of the Confederacy, the Creeks and Seminoles were allowed jointly one representative in the House of Representatives. The Choctaws and Chickasaws were also allowed one representative to be elected alternately from either tribe, and the Cherokees were entitled to a single delegate. These representatives were to serve two year terms, had to be 21 years of age and under no legal disability. The Creek and Seminal delegate had to be a member of either nation. The Cherokee representative was required to be a native born citizen, and the Choctaw and Chickasaw member had to be a tribal member by birth either on the father's or mother's side. (p31)
The delegates were to ensure that the Indians would be able to secure the rights they were entitled to without the intervention of their agents. The delegates were allowed to propose in introduce measures for the benefit of the Indian nations. (p32)
Though the programs outlined for the country were well organized and developed, they were never adequately initiated and maintained. This difference in paper planning and actual execution was the result of many factors. Perhaps the most relevant of these was the continuing devastation of Indian Territory as the opposing armies in advanced and retreated across the country. The dislocation and confusion resulting from the military campaigns made it virtually impossible to establish a civil government with any degree of effectiveness. The Confederacy was hampered also by financial problems from the onset of the Civil War, and early in the conflict the money promised by the South became worthless. Apparently in its haste to gain the much desired Indian alliance, the Confederacy was guilty of promising much more than it could ever deliver. (p33)