have you tried using mencoder?
$ mencoder -oac help
Available codecs:
copy - frame copy, without re-encoding (useful for AC3)
pcm - uncompressed PCM audio
mp3lame - cbr/abr/vbr MP3 using libmp3lame
lavc - FFmpeg audio encoder (MP2, AC3, ...)
check the mencoder manual for more info
or you could use ffmpeg to re-encode the audio to aac