[PlasmaKrab]

One thing to remember:

Casualties are not deaths. That means that one guy drawn off one section by the game engine is just out of order long enough for the game to end, i.e. wounded, immobilized, stunned, you name it.
Admittedly a crowd-control policeman in riot gear should fall out that easily either.

Have you tried reducing drastically the ROF of your stone-throwers? I know that the ROF rating itself doesn't count for much, but if you have something really low like 2 or 3 that should reduce their stone-lugging eagerness. Same if you reduce their experience as well, which should be pretty logical in your setting, wouldn't it?
Then you would have to compromise between them pebbling your soldiers like mad and running off at first sight of an enemy.

Actually (you'd have to check this too) I fear that only actual shooting of the enemy units (here your angry mobs) will have them retreating. Have you tried pushing them off by sheer contact with your Paras? My thought is that they won't budge until at close quarters (whence they will suffer heavy casualties due to the Paras' close-combat bonus), and since the stones are so deadly these days your paras may even end up surredering, which would be ironically ridiculous.

Other solution would be: interlace your stone-throwing mobs with unarmed crowds, here again so as to have less stones thrown at a time.

What are the actual parameters of your stone-throwers and stone-throwing weapon, by the way?