Ballistas work, if they could melt ammo mid-flight then even a marksdwarf would have a problem.
As it is now, it seems ammo in flight is not effected by the world around it, until it bumps into a target or a wall.
If you're lazy, make catapults and use those instead of the ballista, it's usually a long walk to get the wood for the arrows all the way down there, and rocks are everywhere.
If I remember correctly, bolts shot my marksdwarves instantly hit their target, and the bolt path you see is just a special effect. At least in adventure mode, if a bolt is fired, it will hit the target before anyone gets a chance to move, this has been tested to see if a speed 0 dwarf could dodge bolts in adventure mode. If this is true, then it works similar to cave ends, where it hits the end then updates it's location. I have never used ballistas before, but from what I remember of heat transfer from creatures, heat doesn't affect the areas around the creature unless they are wrestling, it just affects the tile they are standing on. Because of this, only water in the tile they are standing in will evaporate.
Also, an easy way to kill SoF is to find freezing water or embark on a glacier. They will walk across the ice, melt it, fall down, and then the ice will refreeze.