In my campaign I use a mechanic where SoD/etc spells deal unrecoverable (or at least slow-recovering) ability drain to boss-type creatures/villains instead of killing/dominating/etc them. Fort-based SoDs are Con drain, Will-based SoDs are Wis drain or Cha drain usually. Its fluffed as the spell killing/dominating/etc only a part of their body or mind. If the ability drain takes them to zero, the spell effect applies as normal. The PCs don't have the major SoDs yet, so I'm not sure how this will play out. The drain should probably be something like 1pt per spell level of the SoD spell used.

I've also toyed with the idea of making the save DCs different for SoD spells than other spells, namely:

For most spells and effects, the save DC would gain a bonus equal to half the caster level/initiator level/HD of ability-user depending on which is appropriate.

For short-duration shut-down spells (paralyzed for 1d4 rounds, etc), the save DC only gains a bonus of a quarter of the level.

For save or dies/long-duration shut-down spells, the save DC gains no bonus and a nat 1 does not auto-fail.

The logic is that by the time SoDs are available, most boss-type creatures that the party would encounter have saves that far exceed the save DCs of most of the party's effects, thus making SoDs a non-option against them but still valid against mooks without shutting down every other spell in the game that allows a save.