At the time, Roman Shtylman, the founder of Bitfloor, described it: “last night, a few of our servers were compromised. As a result, the attacker gained accesses to an unencrypted backup of the wallet keys (the actual keys live in an encrypted area). Using these keys they were able to transfer the coins. This attack took the vast majority of the coins BitFloor was holding on hand.”
So it was a storage issue and had nothing to do with what we're discussing, which is how to process Bitcoin transactions. Which brings me to the question: how would you process transactions on this cold wallet you speak of? Somewhere, you have to have either bitcoind or libbitcoin running (and most business will avoid the latter because it's AGPL, unlike bitcoind which is under MIT license).
To be clear, I strongly agree with the suggestion to keep as much money as possible on cold wallets. If you are just accepting Bitcoins for payment, this can be virtually 100% of your coins. As long as you are regularly moving your coins off of the bitcoind daemon connected to your web app, you are risking very little. Hell, you can transfer the balance off-server every minute if it makes you sleep better.