On a positive note, Apple later released a reference ALAC implementation under the Apache 2.0 license, which includes a patent grant, so the damage is mostly limited to consumer annoyance.
The MPEG-4 format was based on the QuickTime format, so it shouldn't be any surprise that Apple prefers to go with an MPEG-4 format even when an acceptable alternative is available. The reality is that Apple doesn't support very many alternatives to MPEG-4 formats, and they probably wouldn't support MP3 if it weren't for the fact that they wouldn't have been able to take a significant position in the market for digital media players without MP3 playback. The same will probably never be the case for Ogg or FLAC.