Shoot at max resolution, and for most (mosaic-style pixel fields), max JPEG quality: the 2x2 compression corresponds to the maximum color information, so you don't get much loss in image quality vis-a-vis RAW format.
You can then edit the picture and mix down the resolution.
If you do some serious photo adjustments (getting the levels right), you'll end up with a better picture at the lower resoltuion than if you started that way.