I'm not really trying to weigh and decide if 6000+ deaths and forcible removal of 100k+ people from their homes is better or worse than 100 or so years of systemic oppression followed by more, quieter oppression. Instead, I'm looking at this from the perspective of alternatives.

After the Civil War we very nearly had a moment when we could have maybe did something real for racial equality beyond anything we've seen even up to the present day. The Freeman's Bureau was fighting for wages for former slaves, and was generally a force for working class empowerment. Black congressmen were already being voted into office rapidly. If it were left to do its work, it might even have helped to innoculate the Irish- and Italian-Americans against future union busting on Black/White racial lines a few decades down the line.

Instead, after only about a year, Andrew Johnson started fighting and dismantling the Bureau, placing the former slaveowners back into a de facto master/slave relationship with their former slaves, giving the old Southern Democrats back their political power, and generally restoring the status quo as much as possible. The Bureau itself lasted only 5 or 6 years, don't remember. The KKK rose up because reconstruction wasn't there anymore to prevent it, because the Democrats wanted so bad to just put all of the states back in the union and go back to bad old days, and so on.

That was never a realistic moment that I know of in American history where people against war with the native tribes of this land had outsized power and influence. Jackson completely ignoring the Supreme Court's ruling was awful, but while the ruling was grounded in good moral and legal principles, it was, like it or not, extremely unpopular. There wasn't an entire party with a supermajority in Congress that could have kept up the pressure on this issue.