An emblem is a new kind of object, different from a card or a token. It's basically a marker with an ability on it. In fact, the ability is the only characteristic it has. Emblems have no color, name, card type, or anything else—just that ability. They live in the command zone, which is the same place that Archenemy schemes, Planechase planes, Vanguard cards, and EDH generals hang out. They're not permanents, and absolutely nothing can touch them or get rid of them, simply because no cards say that they can.
I think this is a pretty elegant fix, but it'll take a while for the casual players to catch on if they don't push it pretty hard.