With regard to Mexico, we treated it as outright conquest, and made no bones about it. With regard to the Indians, we treated them as sovereign nations, and voluntarily subjected ourselves to our own laws. Big difference there.
...and that government, established with the consent of the governed, entered into a treaty with another group it considered a sovereign nation. You propose to utterly abdicate that treaty; to effectively change the character to that of conquest.
A lot of sovereign nations would consider such a thing--abdicating a treaty and unilaterally declaring sovereignty over their people--to be an act of war.
Congress makes the law. And, as the article pointed out, it did, both in statute and in ratifying a treaty. You're proposing to ignore those laws and treaties.
I don't dispute that it'll make a helluva mess of things to rule in favor of the appellant, but, well, principles are what you do even when the outcome would be inconvenient.
I don't mind having Native Americans obtain sovereignty of the entire United States if by consent of the governed. the problem therefore lies not with the tribes or their treaties, but rather with their forms of government, which are based upon race and heredity.