The idea that a 21st-century sovereign nation would expel a racial minority that had been part of it for a century and a half seems outrageous. Yet this is precisely what has happened in the last month in the Cherokee nation, the second largest American Indian tribe. The US government's condemnatory response, however, may cause more problems than it solves.

The Cherokee freedmen are the descendants of African American slaves owned by wealthy Cherokee tribal members. When principal chief Stand Watie became the last confederate general to surrender in the American civil war, a treaty emancipated these slaves and gave them equal rights. The Cherokee nation went further than this in 1866, amending their constitution as follows:

"All native-born Cherokees, all Indians and whites legally members of the nation by adoption and all freedmen who have been liberated by voluntary act of their former owners or by law […] shall be taken and deemed to be citizens of the Cherokee nation."

But more than a century later, chiefs Ross Swimmer and Wilma Mankiller created a new requirement that all Cherokee should hold a certificate of degree of Indian blood. This stripped the freedmen of citizenship. It was declared unconstitutional in a 2006 decision by the Cherokee supreme court. Chief Chad Smith, an uncompromising opponent of freedmen citizenship, arranged a referendum which, in 2007, amended the constitution of the Cherokee nation to once again require "Indian blood". Last August, this referendum was upheld by the Cherokee supreme court. Two thousand eight hundred freedmen lost their status as citizens, including their right to food aid and medical services. This occurred against the backdrop of a knife-edge election for principal chief, in which freedmen votes would have the potential to change the result.

Some freedmen activists blame the nation's stance on a combination of factors, including racism and an unwillingness to share federal funding or profits accruing from recognised tribal status. However, there is another set of factors that make this a much more nuanced issue. Larry Echo Hawk, assistant secretary for Indian affairs in the US department of the interior, wrote in a widely circulated letter to the acting principal chief Joe Crittenden:

"The department's position is, and has been, that the 1866 treaty between the US and the Cherokee nation vested Cherokee freedmen with rights of citizenship in the nation, including the right of suffrage."

Echo Hawk's threat is that the US federal government will not recognise the outcome of the upcoming election, potentially leading to another constitutional crisis for the Cherokee nation (the last, in 1997, saw a near-coup followed by armed federal intervention). At the same time, the US department of housing and urban development froze $33m (£20.9m) of funds due to the tribe's refusal to reinstate its African American members.

There is a long history of US government attempts to deny the Cherokee's right to self-determination. The most infamous instance is the 1838 ethnic cleansing known as the Trail of Tears, a forced march that killed a quarter of the tribe and an unknown number of their slaves who marched with them. At the turn of the century, the Cherokee constitution was dissolved. This continued as the federal government chose men to act as "chiefs for a day" in order to sign treaties, but otherwise kept the Cherokee nation dormant, and then dragged them through the 1950s federal "termination" policy. The US government interventions were accompanied by boarding schools that forbade the speaking of the Cherokee language, and are part of much wider efforts to kill off Native American cultures. The fear of acculturation is very real, especially given American conservative attacks that modern-day Indians are somehow inauthentic and hence no longer "deserve" treaty rights. Small wonder, then, that the Cherokee should wish to retain the right to determine the criteria for citizenship in their own nation.

It's nevertheless worth noting that the Cherokee are less purist in their approach to race and citizenship than the many tribes that require one-quarter Indian blood for membership. Their use of "linear descent" means there are citizens whose ancestry is only 1/2048 Cherokee. There are many Cherokee citizens with African or Asian ancestry whose citizenship is not being challenged.

If the constitutional amendment is seen to be overturned due to federal bullying – the freedmen have requested the withdrawal of funds that currently pay for food distribution to more than 35,000 households – the idea of self-determination will have taken a heavy blow. More, the hypocrisy of the federal government continuing to support the racial logic of "blood quantum" in other tribes while condemning it here is not lost on anyone. Surely such an outside action will perpetuate, not heal, racial divides within the nation. Self-determination surely means the right to make bad decisions as well as good.

However, none of this excuses the Cherokee nation for its collective decision to exclude the descendants of slaves. Natural justice demands that the citizenship first granted in the 19th century should be upheld without question. Cherokees should celebrate their sovereignty precisely by acknowledging their debt to those whose forced labour helped build Cherokee independence.

The tragedy of the Cherokee supreme court's decision, as Steve Russell argues in a excoriating editorial, is that it achieves what federal government has always wanted. It makes the Cherokee an ethnic special interest group, no longer deserving of the title of "nation".