Calories are going to be a function of alcohol or unfermented sugars. You can lower calories by reducing one or the other or both. But they're kind of dependent on each other.
Looking for low calories by starting with higher gravity (more sugars) wort doesn't make any sense at all to me. Somebody correct me if I'm wrong, but you really can look at your fermenter as a closed system. If your wort has a lot of calories (high sugar content), then you're going to wind up with a high-calorie beer, be it through high alcohol content or more unfermented sugars.
Seems to me the only way to get lower calories is to start with less sugars--essentially lower-calorie wort--which will result in lower ABV or increased dryness (less unfermented sugar because the yeast converts it all to alcohol) or both. Unless you want to re-boil your beer before bottling to cook off some of the alcohol. That would definitely lower the alcohol level and cut a few calories, but it will also kill your yeast so you'd have to force carb (via kegging, basically), and the odds are good you'd get some weird flavors.
If you want low-calorie beer, I would think that making your own is totally the wrong way to go. But that's just me.