Merchants need a way to record transactions immediately. They can't just wait for several confirmations and search the blockchain for a txid. I think gox's proposal should be adopted.
Such merchants are using Bitcoin for something it was not designed to do.
Bitcoin transactions take an hour to confirm, on average.
If you want fast confirmations, you need to build a fast confirmation system on top of Bitcoin. This will likely use semi-trusted third parties that reconcile balances with one another, and can be publicly audited through the blockchain.