Mac OS doesn't read the MKV container, but it should have no problems with MP3 audio together with AVC video.
Does iDVD allow you to specify video and audio from two files? If so, then you can save the audio out to a different format, like AAC and then combine it at authoring time.
I wish VLC would have more solidly identified the audio, instead of saying later 1 2 or 3. Quicktime (even with Perian) seems to only like layer 3. I wonder if the MPEG 2 components for Quicktime widen that support.
iDVD won't let you specify a separate video and audio track, but iMovie will. Workflow would be to import into iMovie the separate audio and video parts, then hit the export to iDVD option.