This problem can easily be fixed by the creation of decentralized exchanges. Currently Waves is working on that and I wish them the best luck in completing that project successfully.
Decentralized exchanges doesnt care about regulations and where in the world
is Carmen Sandiego you are, there is no middle man to create SAR's (Suspicious Activity Reports) and account freezes.
I would like to point out that I dont think Kraken cares about its customers, if they did, they would have invested in Licensing so that they can operate in all 50 states just like I see Bittrex have done, along Coinbase, Bitstamp, and even Ripple(!!) all these exchanges plus much more are wide open not just to New Yorkers, but to all 50 states, but noooo Kraken, Poloniex and Bitfinnex have to be the black sheep not to undergo the licensing process to make themselves available to all 50 states. That's how you know which exchanges are worth it and truly cares about each and everyone of their customers and those mediocre ones that are pick and choose selectives in the name of cheapness refusing to serve customers from a few states.
The real problem is not the license, they are the high fees, that would take them out of the business because they would have to charge it to the users
But some of these exchanges makes so much money that it wouldn't even byte them having to pay for these licenses. Example: Poloniex, dont you tell me that Poloniex makes less money than Bittrex but yes Bittrex managed to have been able to pay for Licensing and I dont see them charging anything special to any New Yorkers or any other states that is affected by licensing issues.
Maybe Kraken might go out of business judging by the number of coins listed there to guestimate their profit levels, but if that held any merit then Bitstamp shouldn't have been able to afford a BitLicense given the fact that they only do Bitcoin and a pesky XRP IOU, not even ethereum, where Kraken does BTX, ETH, ETC, ICN, XRP, and some others so by definition Kraken should be more profitable than Bitstamp and if Bitstamp were able to perfectly afford Licensing so Kraken should have ahd no trouble, and no none of these exchanges that did got licensed are charging anything extra or special to no one, its a free service charging only standard trading fees.