1. Limit it's powers quite specifically (can only obliterate lizardfolk shamans, elf berzerkers, blue-eyed Virgos)
2. Give it a very strong drawback (Suffer half damage inflicted)
3. Reduce the power of the Sceptre so that instead of instant/automatic effects it deals a certain amount of damage instead. If you fail some sort of check, like stamina or whatever and take such and such amount of damage, you are indeed skeletonized.
4. Give it a small number of charges. You can auto-kill anyone with it, but you've only got two shots. Do you feel lucky?