It was a populist law passed in the middle of the Civil War. The entire continent was on fire. And the Cherokee, Choctaw, Seminole, Catawba, and Creek tribes sided with the Confederacy against the United States.
I knew they were opposing the United States (at the time, an aggressively-expansionist neighbour with an order of magnitude more arms manufacturing), but were they all definitely allied with the Confederacy? Your enemies aren't necessarily friends with each other.
(Also, keep in mind: Cherokee, Choctaw, Seminole, Catawba and Creek weren't countries. I vaguely remember that internal Cherokee politics was complicated, and that the US acted as though certain people were representatives when they weren't.)
[1] https://en.wikipedia.org/wiki/Cherokee_in_the_American_Civil...
[2] https://en.wikipedia.org/wiki/Choctaw_Nation_of_Oklahoma#Ame...
In the context of the Cherokee (which I'm more familiar with than other tribes), you initially have a group of mostly-independent city states, surrounded by neighboring tribes (with which there is good and bad history), dealing with substantial population decrease (due to smallpox), trying to negotiate with a fundamentally different culture (colonies/US) encroaching on their lands. Think 10th century Europe.
There were a diversity of opinions on how to move forward, and so a diversity of approaches, as groups jostled for personal advantage. Fundamentally though, it was a delaying action, fought (economically, politically, and militarily) until ceaseless European migration made coexistence as equals untenable.
The Cherokee have a somewhat unique history in that, by the late 1700s, they were moving to colonial style economics (land ownership, farming), politics (central government), language (invention and dissemination of written language in the 1820s), and religion [0].
Unfortunately, 1829 also saw gold discovered in northwest Georgia, at which point there was too much money to be made by seizing and exploiting land, and any burgeoning cultural similarities and human rights were conveniently ignored so fortunes could be made.
[0] https://en.m.wikipedia.org/wiki/New_Echota#History
See also: https://en.m.wikipedia.org/wiki/Cherokee#19th_century
https://en.wikipedia.org/wiki/Native_Americans_in_the_Americ...
(Depending on how many issues you want exclude in over-simplifying the causes of the war.)