You usually don't need your fingers attached to d while proning as you usually first press a movement key and press the prone key afterwards. Due to both animations, proning and unproning, you'll have enough time to switch back to d.
Contrary to proning, you'll use your direction keys a lot when throwing a grenade. That's why space is a better key for that purpose.
And at a certain level, it is almost a necessity to have your wasd fingers dedicated to only that task.
These default controls are supposed to give new players an easier start. They are not made for climbers, who abuse and bypass certain movements, which you don't ever do in other gamemodes.
Anyway, controls changes will probably wait for 1.8, so there's some time left to keep discussing.