David Weber's books have given me the impression that you reload it by lying your back and cocking it with your feet, before poking your head up out of your ice hole to shoot again at the Temple Guardsmen. Seems reasonable but I don't know if it would work in practice. In any case, that's about reloading instead of aiming.
Maybe crossbows should have a ROF penalty while prone instead of disadvantage to attack rolls?
I agree that it leads to good play. Generally I feel like anything that helps justify the existence of melee characters is a good thing. If someone is lying prone to avoid missile fire, presenting a melee threat is one way to punish them for that.
That said, most of my tool-using bad guys are not disciplined enough to do that kind of thing. Mostly just scro and hobgoblins. (Maybe I should add drow to that list but historically I haven't played drow as disciplined team fighters, rather than chaotic individualists.)