In theory, I agree, but in practice we really can't allow this to happen. Its not about ANTIFA, its about the people who suddenly find their homes and businesses inside these "autonomous zones". The Government has a duty to not let these things happen. The mayors of these cities have a duty. And if they fail in it, then the Governor has a duty. Note that nobody in a Red State is threatening to set up these autonomous zones. Its only in areas where both the city and the state are controlled by the Democrats. This is a shocking abrogation of Responsibility, and a foretaste for what will happen to America writ large if the Democrats regain control of the Federal Government.
They desperately want to force Trumps hand though. And there is a way to do it too. Send a couple of uniformed ATF officers to the "freezone" and have them try and walk in, calm as you please. The moment the protestors stop them from entering, when combined with their own fricking sign at the "border" claiming the area beyond is outside the United States, they are in violation of
section 2383 of title 18.
At which point the President can invoke the insurrection act, give the "protestors" 24 hours to leave, and then send in the US Marshals, ATF and FBI. Anyone still there after the 24 hours have elapsed can be arrested and spend the next decade in federal prison. I doubt the Army would actually be required to put this down. Federal Police can do it.