I wouldn't begin to read their (Cherokee) minds, or even attempt to. It's possible, of course, but even
if they were attracted to the cause, you have to know that the prior acts against the Cherokee by the Federal government would color their perception as to whom they should throw in with. Having similar reasons for hating someone enough to go to war with them doesn't necessarily imply philosophical agreement between the allied parties, especially when prior historical events could influence the decision making of one of the groups so heavily. To use a more modern analogy, I don't think anyone would say "the Arabs are now pro-West" or even that the Kuwaitis are now pro-West simply because Kuwait allowed us to attack Iraq from there. Both of us wanted Saddam out, for different reasons. Combining those reasons into one cohesive philosophy in the way the author does with the Cherokee and Confederacy is disingenuous, I believe.
My point, which apparently I'm doing a poor job of making, is that the article seems to ignore any fact or relevent history that won't support the author's claims that the Feds were wrong and the Confederates were right and the Cherokee "support" for the Confederacy proves that. As I stated, instead of support for the Confederacy, it could have been more a case of "the enemy of my enemy is my friend". His (the author) failure to write a decent article doesn't disprove any theories he may have, but it certainly doesn't benefit his cause either.
Hmm, you seem to miss that the Feds were wrong.