You repay any USD-deposits, since they are all in tact.
You then re-pay what you can of the remaining BTC deposits.
Customer assets are customer assets. It doesn't matter if they are dollars, bitcoins or bananas. If BitFloor does not have reserves (and that was reported in OP) or any other way to make customers whole, then this is a bankruptcy case. This exchange is operating in the U.S., there are very specific laws as to how to proceed.
Disbursing funds to some customers and not others would be a criminal act under those.
I believe a court order (injunction) should be filed to help ensure the exchange operator proceeds as prescribed by law.
[Edited, s/funds/assets/. and added.]