It looks like the Alliance truly ceased to exist. Anderson's gesture is more symbolic than anything. How could his words have any power if he stays back on Earth? Soon, the Reapers will block the orbit and cut off all communications between the Earth and the rest of the galaxy. Anderson is heading into the enemy territory and he gives Shepard his status back?
Looks like a last-ditch attempt to get Shepard's loyalty back. That, or Anderson is trying to make Shepard follow his orders, and how could you do so if Shepard's not with the Alliance? He's pulling the rank, so to speak - pulling on the last remaining string that connects him to Shepard. Maybe Shepard didn't want to leave Anderson here. Or maybe Shepard didn't want to leave the Earth. In any case, it's a very cold good-bye, since Shepard isn't bound to follow anyone's orders anymore, with the Alliance or not, and Anderson is a jerk.
That's right, Shepard, step aside, Anderson wants to be a self-sacrificing hero, and you're interfering with his biggest dream. Maybe he hates Shepard now, for working with Cerberus to save those colonies. Maybe he thinks it's something he should've done. Or maybe he's just tired from inaction ever since being forcibly retired in ME1, and he's impatient to start fighting.
Anyway, Anderson carries Shepard's dog tags with him? Aww, how sweet. Looks like Shepard was stripped of his rank after all, during the trial. Maybe they even officially expelled him from the Alliance, during the sentence. And confiscated his dog tags.