I think conflict does a lot to offset this. Also, the risk of rolling black pips makes it all the more dangerous.
Above all, one-shotting an exciting nemesis makes for a boring game. The villains get away to terrorize the PCs another day, remember?
If you want the NPC to stick around, do a deus ex and pull the chute. When it makes sense and feels right to have them die it will be more satisfying for the PCs.