Ok, Orecchiette version 0.3.6 is now working its way up into extras-devel. There is now an option (hidden rather deep ) in the Preferences panel, called "Combined Audio Recording Options", which will allow you to assign the microphone and speaker audio streams to separate recorded stereo channels. There are three options available, "Microphone and Speaker Centered", "Microphone Left, Speaker Right", and "Microphone Right, Speaker Left".

I have tested a little bit, and it seems to work correctly for standard (non-phone) audio recording. I don't have my N900s connected to a cell provider any more, so I can't really test the phone recording adequately, but I believe it should work in an identical fashion. Please inform me if you find any problems with this version. Thanks!