You can dither the track to 44.1 if you want, but if the reference track is an mp3 you run the risk of introducing artifacts. Best is if iTunes offers a download choice, then definitely download the ref track at 44.1k.

Some people are able to run the 11r at 48k just fine, though some people have reported some issues with this (just search clock or 48khz on here to see what I mean).

I would run the 11r at 48k, and then if you run into issues then dither and re-bounce the ref track to 44.1k and run the 11r at 44.1k.

edit: actually, the prob might have been with the 44.1k setting but I can't remember.. 48k should be fine..