The irony is that if these AZs were permitted it could give said segregationists exactly what they had been after for decades.
In terms of declaring themselves "autonomous", I'm thinking (and I imagine others in power are thinking as well) that this is simply done as a statement of protest, rather than an actual serious attempt to form a sovereign government. So crushing this without mercy is politically infeasable, especially given that the whole protest is about police and justice reform. I don't think this sets any kind of legal precedent. Better let them make the statement and let it run its course on its own.