I'd start with Allegiance to represent the chance of divine intervention. The prayers might be equivalent to spells that require an Allegiance roll, or might be skills in their own right capped by Allegiance.
The one problem I see is that some prayers cost more Character Points than others, representing more profound effects. That probably would translate to a system of "levels". What the "levels" mean is the big question:
- Each level represents an increase in difficulty; level 1 is a straight Allegiance roll, level 2 is Allegiance x 1/2, level 3 is Allegiance x1/5, and so on.
- Each higher level prayer requires knowledge of lower level prayers, either specifically or generally. For example, the maximum number of prayers at level N is one less than the number of prayers at level N-1. Thus if you want a Level 3 prayer you'll need 2 level 2s and 3 level 1s.
- Prayers require a number of Piety Points equal to the prayer level. Priests earn Piety through sacrifices (e.g. animals or wealth), services to their religion, or divine quests.
- Higher level prayers require higher rank in one's religion, which means greater duties and greater expectations.
Take a look at Theism in RuneQuest 6th edition, which incorporates the latter two mechanisms. Curiously, HarnMaster Religion is remarkably similar.
"A hidden corridor! Fortunately it was labeled!" -- Sadie Doyle, "Beyond Belief: Sarcophagus Now", The Thrilling Adventure Hour