How does an empty block (~250 bytes) do you more harm than any other 250 byte, 25BTC transaction?  [All I can see is that it (slightly) increases the difficulty two weeks from today.  But if it included one or more transactions, it would still (slightly) increase the difficulty two weeks from today.]  Yes, it's a lost opportunity to include transactions, but is it really any worse than if the miner hadn't been mining at all?

If it ain't broke, don't fix it.