Yes, you can make a change such as this by using the ADVANCED SPEAKER settings. This settings menu allows you to define custom speaker configurations and bass management settings based on the surround mode. So you could in theory set up your receiver to play Dolby Digital and dts soundtracks using all SMALL loudspeakers with a Subwoofer, and configure Stereo sources to play with just 2 LARGE front speakers and no subwoofer.

The Advanced Speaker settings menu is located with the SPEAKER setup menu of the On Screen Display.