Harmony does have Apple remote code
I've had a Logitech Harmony for the last 6 months, and when I initially got it, I uploaded the Apple Remote instructions to it. Worked great on my iMac and MacBook Pro and handled all the comands that the Apple remote could. Now that I have an AppleTV, I was able to include it in my theatre system and low and behold, my Harmony picked up where the AppleTV remote left off.
All the apple remotes are the same, there's nothing special about the one that comes with AppleTV. You can take that and use it on any existing (Intel) Mac and it will work just the same as the one that came with the computer.