Does QuickTime automatically record stereo audio into mono

Well, seems like I just had to think about it a little bit more. My workaround is not possible using only system utilities. I used Soundflower and LineIn from Rogue Amoeba software.

Using LineIn, I could select channels 3-4 specifically from the PreSonus device and route those to the two-channel Soundflower device. Then, I simply selected the Soundflower device as my input in iChat.

whenever I record audio in QuickTime

This is the problem. QuickTime doesn't offer the ability to change the recording type or to pan inputs to a particular track in the recording when you're making it. It records stereo. And it captures one input left, the other input right. I just tried it out with my Duet and, no matter where I set the pan on the mic input in the Maestro mix console, QuickTime captured that signal input on the left channel only.

The solution, I'm afraid, is to stop using QuickTime.

Garageband, which is likely already on your Mac, will let you capture a mono source and then pan and bounce a master mix with the mono source placed in any location you like in the stereo field. It definitely is a more suitable interface for capturing and manipulating audio than QuickTime.