I think what you're really looking for is MKVtools. It will take your MKV files and demux them, convert the audio to AAC and remux all without re-encoding your video! It literally takes about 10 minutes for a full length movie on my macpro.
It will also handle subtitles, but I havent messed with that feature in length.
http://www.emmgunn.com/mokgvm2dvd/mokgvmhome.html