Originally, I thought about clerics "turning" spells as undead with hit dice equal to the spell's level. But if we restrict clerics to purely defensive, commanding, healing, and dispelling magic, we can eliminate the spell list entirely (except as an alternative magical spell list.)
- Defense: Use the hit dice of the enemy for the Turn Undead roll. Area of effect is one person + half the cleric's hit dice, in feet (round down.)
- Command: Use the hit dice of a supernatural enemy for the Turn Undead roll. Double hit dice for natural animal, triple for plant, quadruple for sentient being; command must be simple and defensive in nature.
- Healing: Cleric defines how big of a wound to heal in terms of hit dice, but this can only be done once per day per person.
- Disease: Compare the disease effects to undead powers; trivial ailments are 1 HD (like zombies,) paralysis is 2 HD (like ghouls,) serious or deadly diseases are 3 or 4 HD, and anything as bad as a mummy's curse is 5 HD. You can treat "death" (for raising the dead) as being at least equivalent to a mummy and poison as one step below (4 HD.)
- Dispelling: Use the level of an evil spell effect as its hit dice. Can only be attempted once per day per spell effect, and it might not last.
- Warning: Traps and non-living dangers can be rated in terms of damage dice, which can be used as HD when praying for knowledge of nearby dangers.
I would keep the exact penalty secret, because that allows me to leave the question of "which religion/deity is the true one?" open. The cleric doesn't know if prayer works because the deity or deities are listening, or if it's just a matter of convincing minor spirits to obey.
Edit: See More on Clerics Without Spells for further thoughts, Paladins Without Spells for an application of the same mechanic to another class, and White Magicians for spellcasters who use the now-orphaned Cleric spells.