MPlayer uses ffmpeg and other libraries internally, so it doesn't use anything external or part of the OS. I much prefer MPlayer in every respect to VLC.

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.