Quicktime is not re-encoding the mp3 but rather is saving the encoded file inside the .mov wrapper. You should notice that the save is almost instantaneous and you would never see that if any kind of encoding were occuring. Encoding is time intensive.
Actually, Quicktime does not "Save" anything in its original file structure unless that file structure was .mov. It creates new material in non-mov format only by "Exporting" it
You might want to take a look at Audacity, a freeware sound utility that can be extended to encode mp3 files:
Audacity