the debaying is probably happening in the DSLR_RAW module (as the images are opened) where it's probably currently turned on...
if you want to calibrate the images without changing the DSLR_RAW settings, you should be running ImageCalibration and giving the format hint "raw cfa" to ImageCalibration. then you would run Debayer, and then StarAlignment, and then ImageIntegration.
if you use BPP i think it will set up as described above on its own.
rob