I don't understand how any bitcoin exchange can maintain that they are only conducting business in a home/primary State while they are knowingly serving residents across borders. I suppose the exchange could establish procedures to filter residents. For example, not allowing unverified accounts and only approving accounts of residents where the exchange is registered. But, this policy would severely cripple an exchange's ability to compete with other exchanges that are registered in every State.
Every bitcoin exchange should be seeking registration with every State. Simple as that. It might be expensive and time consuming, but that's the cost of running a money services business that extends across State borders.
The problem doesn't end there, because if they don't have a way of filtering where their users live then they'll potentially be doing business in all kinds of other countries, and breaking their laws as well.
The ideal solution would be to get the necessary permits for every jurisdiction in the world, but this may not be practical - for example, there are a lot of countries where PayPal can't do business, presumably not for lack of trying.
I think the upshot is that (above-the-radar) exchanges will need some way of filtering their customers by jurisdiction. IANAL, but it may be enough just to geolocate their IPs and ask them to promise that they're in one of the places where the exchange is licensed. Once they've done that, there's no particular need to operate everywhere in the US either. It may actually be less risky to have a lot of little exchanges in different states rather than one big national one, so you don't risk getting everyone's service disrupted because you messed up the paperwork for North Dakota or whatever.