The ability damage for a spell like Flesh to Stone is a good idea. Another thought that has been going around inside my head for a little while is to make the casting of save or die spells dangerous to the caster as well as to the target. This would be represented by the spellcaster being forced to pass a Will save vs the spell DC or suffer some sort of negative effect. For example, a 14th level necromancer with a 18 Int and Spell Focus: Necromancy casts Finger of Death at his opponent. The opponent must make a Fort save (DC 21) or die, if he save he takes 3d6+14 damage. The necromancer must then make a Will save (DC 21) or take 3d6+14 damage, if he succeeds he takes nothing.

Anyway, I think its a way to both add some extra tension to save or die spells and to make the spell caster think twice before using them.