So, with the changes to the deities themselves, in that they are bare echoes of their former power, Cleric as a class has to go through some minor changes for several reasons.
Aura: Previously, Clerics of a particular alignment radiated that alignment as an aura. Since alignment no longer exists, the need for this class feature is removed.
Domains: Here is the most drastic change. Though Tavost, god of justice still exists, his sacrifice to become the first echo god had a profound change on the pantheon. Every deity was granted the Retribution domain, and to this day, it affects the clerics of the faithful. Every cleric must select Retribution as one of their core domains.
Spontaneous casting/Channel Energy: Remove alignment restrictions, as alignments no longer exist. Clerics choose each day whether to channel positive or negative energy for Spontaneous casting and Channel Energy.
Spells: A cleric is a conduit for divine energy. However, that divine energy has gone from a roaring fire to a flickering candle. Clerics still cast spells of equal power to the glory days of the gods, but they recover them much more slowly. A cleric is only able to recover as many spell levels per day equal to their level in the cleric class. Domain spell slots are unaffected, and refresh normally. This represents a weakness for player Clerics, which will have to be balanced.
Gift of the believer: To balance the change to spells, Clerics are given strange gifts for their devotion. Clerics may choose one of the following gifts. This gift can be changed at each even numbered level. Unless otherwise stated, you may use your ability as many times per day as 1+your wisdom modifier. THESE ARE ROUGH DRAFTS, and i would appreciate feedback on how to fix any glaring problems.
Castigation: You may smite the faithless.To affect the target, you must speak words of holy vengeance and touch the target. You deal damage equal to your cleric level, and no energy resistance or saving throw against this damage applies. Damage reduction applies normally, but this attack counts as if used my a magic or psionic weapon.
Proscription: You may touch a faithless target and forbid them from harming any being for 1d4 rounds. A will save reduces this to one round, and no being may be the target of this ability more than once per day. The dc is 10+ 1/2 your cleric level + your wisdom modifier.
Abnegation: A cleric can use this ability only when he takes no standard action in his turn. Instead, he donates his standard action to an ally within 30 feet, who may then take an extra standard action in his turn.
Dereliction: With a successful touch attack, you can force an enemy to take either a move action next turn, or a standard action, but not both as normal. There is no save against this ability.
Ascension: You gain wings of divine power, and you are able to fly for 1 minute per level of the cleric class you have. you may use this ability in 1 minute increments, and the total duration refreshes when you next gain spells.