I recommend using SoX like this:
sox <input> <output> tempo 0.5
This slows down <input>'s tempo by a factor of 2 and record the result to <output>.
You can add option --show-progress to display relevant information and progression percentage.
Note that if <input> is for instance normal.wav and <output> is half-tempo.ogg, SoX will detect the different audio encoding by itself (for more control on that part, read man sox).
The tempo algorithm should give similar results to VLC's scaletempo module. However you can try the alternative stretch algorithm:
sox <input> <output> stretch 2
The result is expected to be more synthetic (again, read man sox for details) and be aware that the parameter is the inverse of the one given to tempo (2 instead of 0.5 in this example).
SoX offers even more possibilities of time manipulation through speed, pitch and bend options that can be easily explored.
To install SoX using apt-get:
sudo apt-get install sox
To enable extra codecs (including MP3), add this library:
sudo apt-get install libsox-fmt-all
As a final note, I would come back to VLC since you can play your file slowed down from command line this way:
cvlc --rate 0.5 <input>
So there may be a way to ask VLC to save the result to some file, or to output audio to JACK and then use a JACK compatible recorder.