marcão,
olha só o que achei nos meus "arquivos":
BeSweetGUI profile for AC3 -> MP2
besweet -core( -input in.ac3 -output out.mp2 -logfile BeSweet.log )
-azid( -n1 -c normal -s surround2 -L -3db -g max ) -ota( -d xx )
-mp2enc( -b 224 -m s -e )
ps: change the "224" to desired bitrate!

maybe you don't want to use surround2 and also
you may have or have not a delay of xx ms.
Also, leave out the -n1 if you deal with a 2 channel AC3.
...about 44,1 kHz. :
add '-shibatch( --rate 44100 )' which does the downsampling.
troca os ".ac3" por ".wav".....sacou?
este é "mais legal" :
How to HeadAC3he 5.1 AC3 rip to six discreet .wavs?
(assume that you would get six separate .wav files
after HeadAC3he does it's thing!)
use the command line utility azid.
Enter as follows:
azid -d3/2 -oX Filename.ac3 X.wav
X represents the channel you want to decode;
i.e, l for left, sl for surround left etc.
ajuda?
.....mais "possibilidades" :
GUIDE: High Quality Stereo waves from DTS
http://forum.doom9.org/showthread.php?s=&threadid=51542
e
Extract AC3 tracks with SmartRipper:
http://dvd.box.sk/index.php?pid=guid&prj=view&rid=12