Ken --

The general conditions cited in your post are reasonably specific and should answer the original question. Indians involved in the removal such as the Creeks, Cherokees, Choctaws, Chickasaws and Seminoles were often more Southern in culture so it doesn't take much to explain their affinity to the Confederate cause.

It's more difficult to explain the Ross faction's willingness to align themselves with the Federal government. It's easier to understand that within the context of internal struggles for power among the Indians themselves.

With regard to the mayhem and murder mentioned in earlier posts, a premature end to the war might have left some problems unresolved. For instance, it would be interesting to learn how many people in Kansas wished to completely be rid of their Southern neighbors. In a more 'civilized' theater of war, "Uncle Billy" Sherman wrote about measures to be taken against Southern civilians --

Until we can repopulate Georgia, it is useless for us to occupy it ---

Since Kansas experienced such an influx of settlers from Southern states in the 1850s, I would not be surprised to learn that other Kansas residents were anxious for all Southerners and other undesirables to be gone forever, one way or another.