In lieu of any guidelines this is what I have come up with:
The first spell of each level is chosen by the Cleric's Player.
The second spell of each level is chosen by the Judge.
The third spell of each level is randomized (permanently).
The fourth spell of each level is randomized as a "daily".
For the first choice the Judge is encouraged to agree to whatever choice the player is making, unless it goes directly against the deity's ethos, and the player can't come up with a cool plan for why he should get it anyway. (A Sun god granting darkness for instance: "don't forget that the divinatory power of lunar eclipses ultimately come from the sun...")
The Judge will naturally select a spell appropriate for the god. Don't be afraid to choose a spell that will challenge the player to come up with constructive usages.
The totally random spell (like a DCC Wizard's spells) is only rolled AFTER the player and the Judge makes their choices. If you roll a duplicate (the same as the player's or Judge's choices) I would be inclined to generosity, and consider it a daily spell (see below) that just happens to hold the "no spell" spell right now.
A "daily" is a spell "slot" that CAN function much like D&D prepared spellcasting in that at a given time of day (sunrise, midnight etc) the Cleric can pray for a new spell to replace the old one. Asking for a new spell should be considered a much bigger deal than in D&D, though. Whenever there's no pressing reason why the existing spell can't suffice, the Cleric should not ask for a change. But "our quest takes us into the Desert so I humbly ask for something else than Water Breathing" might be considered a valid request
Whether the new spell is determined to be one the Cleric actually asks for, or just a random one, is up to the Judge. If the Cleric asks for a spell genuinely useful to further the deity's goals, she should likely get it. If the Cleric just pesters his god for the "best" spell repeatedly, the Judge should feel free to grant him the "no spell" spell
At higher levels, Clerics gain more than four spells of a given level. I would probably randomize these spells much like the third spell: if you get a duplicate result, that "slot" is permanently a "daily"; while if you get a new spell, that is your permanent new ability.
This would result in a guaranteed degree of player agency, a guaranteed influence from the Judge, and a guaranteed chance of wacky randomness!
Thoughts? Mistakes? Things I should have taken into consideration?