My new Apple TV (2nd gen) works fine so far with my Harmony 670. I had to try a few different categories in the Harmony database before I got a match for "Apple TV". I don't remember now where it actually was, maybe something like "PC media server".
I was puzzled at first because several more buttons are listed than are actually on the remote that comes with the Apple TV, but at least some of them do work. For example, Harmony's "fast forward" and "rewind" buttons work when playing video, even though the Apple remote doesn't have them. I haven't tried all of the "extra" buttons yet.