I personally don't think that throwing, in and of itself, is overpowered. Non-siege projectiles are what need to be toned down.
Throwing doesn't need to be toned down, just made more realistic. Such as myself creating a new character today, and going into a human armour shop. My actions are as follows:
I find the shop.
I pick up the 3000 copper coins in the chest.
I bash the shopkeeper if I'm not a malicious race and then 'give' a few coins back to him Elfen Lied vector style.
His lung, kidney, spleen, heart, and whatnot are pierced.
He either dies or I bash into him a bit more.
I go 'shopping'.
I promptly kill the whole town. (If your smart you don't die from child swarms.)
And I sometimes may get totally pwnt by a kobold. Oh dear. I have to spend a few minutes typing g, a (Repeat 600), then t, c, <enter> (Repeat 600).
And there is the general steal from town, kill all encounter. I don't think ranged should be down toned, because it is hard to train, requires ammunition, and yes, a fast flying steel bolt or arrow will pierce through your armor sometimes, or hit you in an unprotected area and totally maim you. This is not unrealistic. They should only make the throwing do more damage based on material. Yes this means you probably can't main people with high-speed water or blood, but as a legendary thrower you would still be able to pierce someone's brain or bruise them with a coin. Just not total maimage.