Tom, in response to your question: "One thing I still don't quite understand is, after all the U.S. government had done to the Cherokee's ('trail of tears', etc.), what would possibly motivate them to become 'pro-union', or 'pro-confederate', for that matter?"

You have a good point, the so called 'pro-union' or 'loyal' Cherokee were much more anti-Southern Cherokee. They generally distrusted the US Government. The Cherokee and Creek Nations still had smoldering issues over the removals where one faction of the tribe believed removal was inevitable and negotiated the best treaty they could get and the other faction tried to hold out and then blamed the "treaty signers" when they were removed by force. When the US began to split, the Cherokee began to split generally along the old Treaty Party vs Ross Party lines. The former Treaty Party, upper economic class, mixed bloods, whites, and slave owners were predominately Southern Cherokee. The Ross Party, traditionalist Cherokee (called full bloods though this relates more to conviction that to genetics) were "anti-Southern Cherokee". There where many murders and attacks on each other after the removals. There was also a struggle for political power.

As to why the tribe signed the treaty with the Confederacty, the simple answer is "survival". They were not going to be allowed to remain neutral.

The Arkansas River connected the Cherokee economically to the South. They were culturally closer to the South than the North. The white citizens of the tribe were from the South and the extended families of the mixed bloods where generally from the South. (Remember that "Cherokee" is not a race, it is a nationality and there were many mixed blood, white, black, and hispanic citizens).

Cherokee annuities were invested in Southern Banks. The Indian Agents were predominately 'Southern Men" and used their influence on the tribes. Some Cherokee owned slaves. The missionaries were generally from the North and abolitionists. Speaking still in broad generalities, the mixed bloods had more Southern Baptists and the full bloods had more Northern Baptists.

The US promised protection to the tribes but then abandoned the Indian Territory in May 1861. The Confederacy won the battles of Manassas VA (1st Bull Run) and Oak Hills MO (Wilson's Creek). Confederate Troops were in Missouri, Arkansas, and Texas. Kansans were jayhawking in the Cherokee Nation, predominately stealing cattle. Kansans were also viewed as chronic squatters on Cherokee land.

I have to keep repeating these are broad generalities, not absolutes. The terms of the Treaty with the Confederacy (contained in the Official Records) gives an indication of what was important to the Cherokee as a nation. The 'pro-Union' Cherokee agreed to the Confederate Treaty under duress and later defected and joined the Union Indian Home Guards.