Afaik iTunes is not trancoding (which would be required of course to modify the source). I can't guarantee it but some folks that should know tell me thats the case.
The response I got over at AVS indicates that Apple TV 2 would convert my 16/44.1 ALAC files to 48 khz. I guess there is some debate as to whether or not this affects the sound quality. Thread here if you're interested.
Hammie's set up is a lot more refined that mine is. I ditched my Anthem pre/pro and amp about 2 years ago and have been using a Denon 4810 as my AVR. All of my sources connect to it via HDMI and then HDMI out to my plasma. I really was set on selling my mini since it rarely gets used for anything except some ALAC playback through iTunes maybe 1-2x a month. Now I'm not so sure if I'll sell it.