busoni, you need to shut down Poloniex now and try to make your users whole from your own funds and debt. Do not continue trying to run an exchange. Your post mortem indicates that you do not have sufficient programming ability to handle other peoples money - no mention was even made of database transactions, which are a basic "database programming 101" topic. Your proposed fix of checking for negative balances is wrong and indicates that your code is almost certainly riddled with other exploitable bugs.

Please do the right thing and refund everyones outstanding balances, then wind up your operation.