My opinion on the matter is that there are better things to worry about than hacking up bitcoind to earn a few extra bitcents. I also believe that the way that bitcoind is written is kinda smart, it allows the market itself to dictate the transaction fee price.
Any small to medium sized pool that actually thinks that they can make a net profit off of transaction fees is probably misleading themselves. Because of this, I'd rather spend my efforts improving my pool in-general and trying to create worthwhile "value-add" features that my members would be willing to pay for, than to hack-up bitcoind to exclude free transaction.
Again, just my opinion on the matter.