Can the per-image mean and median stats be calculated separately for positive and negative classified objects and exported in the ImageData summary file?
I think what you would need to do here is to create two object sets (one for positive, one for negative) using FilterObjects and then apply the same measurements to both object sets. That way, when you check off the median and mean evaluation boxes in ExportToSpreadsheet, you should get columns in the per-image table with the same measurements but corresponding to different objects.
Does this get you what you are looking for? Or is the question how to create the positive/negative objects?