I'd say in the short term the weight loss medications would work as it sounds like trying to fiddle with the exercise dynamic might be worthy of a specific update, etc.
Maybe even adding such options to the leveling system to keep things fair.
After checking the code I found a bug that meant exercise wasn't causing as much weight loss as it should (which is now fixed). As I was changing this code, I decided to buff the calories burned when exercising alone as it was the quickest, easiest solution to help players manage their weight until something better can be added.
I think your idea about options in the leveling system might be on the right track. Part of the problem is that the calorie counts of all the food gets massively increased from all the upgrades you can unlock, but the exercise calories remain static (although I do have it so that the larger you are the more calories you burn from exercising).