So this year I've stopped working out, and my grades have improved drastically, but at the cost of losing muscle mass and gaining fat, and becoming physically slower and lazier just as I became faster and more active intellectually. One effect I especially noticed was the disappearance of that perpetual state of happiness/satisfaction that comes from frequent physical exertion, which I think had a tendency to get in the way of a feeling of urgency regarding studies; why bother with tiresome and frustrating intellectual exercise when physical exercise yielded results and pleasure/satisfaction much more easily and reliably?

Are you sure there isn't another factor causing improved grades? My impression was that it was pretty well-established that exercise improves mental performance.

Or possibly it's the amount of time you spent exercising, which gave you less time to do other things? Were you spending a lot of time working out? If so, you may want to look into high-intensity interval training to get the benefits of physical exercise in as little time as possible.

Another idea: save your workouts for the end of the day, so you don't have the post-workout feeling all day and will still feel like you need to get stuff done?