Try to use another streaming device instead of your 48khz Apple TV. Yes reclockers will help but it won't solve the main problem which is the resampling of 44.1khz to 48khz. Most music today is 44.1khz - stay with the 44.1khz, 88.2khz, 176.2khz, and 352.8khz rates for audio. Don't let any device resample it to other frequencies.
Apple TV - 44.1 kHz output
I have read in multiple places that the Apple TV outputs in 48 kHz; however, looking at my Audio Midi Setup on my new MacBook Pro the only listed option is 44.1 kHz / 16 bit for AirPlay to the Apple TV. The same option is available for the Apple Airport Extreme AirPlay output. Ironically, there are options to increase the bit depth for the internal speakers.
Maybe things have changed as I have a new Macbook Pro and Apple TV.
Maybe things have changed as I have a new Macbook Pro and Apple TV.