You might have a look at sox (which also comes with soxmix) - I'm not sure if it is actually able to mix two sources to different channels, but since you asked for a scriptable audio editor, sox has been the first thing that came in my mind, as it is scriptable as in shell script. Many people think of sox as just a tool to convert from one audio format to another, but actually sox can do *much* more and is probably the best choice when it comes to things that should be done more or less often.
