This has been a great lesson for me, trust me.
Then why are you trying to run an exchange based on previously compromised code?
Most of the code is new. You can feel that because of the way orders are executed on bitfinex: they are absolutely not executed like in bitcoinica. orders are matched against real orders, can be and are often partially filled (like on mtgox when you execute an order), instead of being executed in full against an arbitrary ticker price like bitcoinica orders.
The code don't use float numbers, we checked against possible race conditions (did have some previous week and that allow us to update the code), we added all the input controls that we could, we simplified and rewrited workers...
Plus, finally, even if the server is compromised, there is nothing on it that would let a hacker steal bitcoins or usd, from the wallets (which is readonly) nor from mtgox (the api key doesn't allow that).
So seriously, it is secure.
Now believe what you want, I'm returning to my work on improving the website with new features.
Raphael