But why bother if the target is not an iPod? ALAC offers nothing else over FLAC. Both are lossless compressions, with full metadata. Both are well-supported. Compression ratios about the same, which is why the file sizes are not really different.
ALAC however is the only lossless compressed format that an iPod without modifying the software will play, and that only at 48000. Since 96000 --> 48000 is an exact half-sample (technically this is a decimation, actually should be called a binamation, but that's not a word), the loss will most likely be unaudible on most tracks, which you can easily test by playing the 48000 file (even a FLAC 48000) on your PC.