I posted this elsewhere, but it is probably my favorite solution so far, far from perfect, but still;
Categorising the weapons themselves might work out for the best (much like how armors effect sneak), light weapons could be carried in hand for no sneak minus (this could include light weapons that bring you out of stealth when fired too), medium weapons which inflict a malus to sneak when wielded in hand, and heavy weapons, which make sneak impossible when wielded in hands, and which break sneak when equipped.