Unfortunately that's what we're working with. Ken is aware of that issue just as much as anyone else. It's just a matter of time before the same problem happens, but you've got to admit that bitfunder and btct were the big dogs, easier to find. Ken's just buying some more time, that's all that can be done. He's ambitiously working on a more viable alternative, whether it's color coins or ripple based.
If the transfer of shares is going to scare you, you might want to sell. If not, with the rise of BTC value, the mining ROI is increasing which can only help ACTM.
There won't be any market trading until colored coins are implemented, so I don't see it getting shut down. If anyone gets colored coins working in production then the other exchanges would follow closely... after all it is open source if it's going to use the Bitcoin blockchain (unless AM came up with a whole new coin, but colored coins certainly seem like a better idea). I think theoretically this would also allow shares to be moved from one exchange to another and enable efficient arbitrage that was impossible with BTC-TC and Bitfunder's centralized approach.