The Cleric class is one of the most problematic because it has the potential to be very interesting or very uninteresting depending on how it's executed in the setting. In a detailed in campaign world there is usually a detailed and balanced pantheon of Gods (or whatnot) for clerics to play off of. In a minimalist campaign there usually isn't a lot of thought put into it and generic gods are pulled out. In both cases there can a be a problem because in the detailed world all these divine entities would require custom versions of the cleric to carry their various philosophies/powers into the world - something not much supported in the general rules. In the minimalist campaign the Cleric is simply is the holy magic guy - an armour wearing magic user who heals and touts the laws of a generic god - something which is supported in the rules but can be a drag. The SRD is least helpful in this, as a lot of cleric spells are duplicates of magic user spells anyway - so the perception of is reinforced. Sure all this can be overcome by good players and GMs in either instance, but I think that the deck is stacked against it. Ideally a cleric spell list would be a list of spells rituals that derived from their religion and the more religions in the setting the more spells and rituals you would have to deal with. That's hard on the GM and hard on the players however and I tip my hat to those that can pull it off well. I can't offer many solutions to this here. I did have the idea of making the cleric spells over entirely but I am trying to make Beacon as compatible with d20 references as I can so I settled with working over the SRD spells, trying to find ways to highlight the class. I did put back in a lot of dualism in the spells which I think follows from the older game - I can't recall if there was an actual cause light woulds in old d&d spell lists but it was implied (or imagined) a bad cleric could reverse the cure spells.
In Beacon, Arcane magic is the magic of Words, Divine magic is the magic of Souls. The spells come from outside the caster and can be channeled by will alone. Divine magic spells can be made into potions, they can be imbued into objects - but they cannot be written down. Following from this a cleric can't add spells to their spell book - they either simply know all the spells as a product of their faith or have had religious training to access them. I am willing to go either way on this - perhaps a mixture of the two if I was running the campaign.
As for the holy avenger role - in D&D the paladin fills that role, something that always bugged me. I mean isn't the cleric really supposed to be the paladin? If he wasn't he wouldn't be allowed to wear plate armour and beat the hell out of things- he'd be in the back with the wizards. They needed a whole other class just because they won't let the poor bastard use sharp objects?
So a Beacon Cleric can use sharp objects (unless his faith prohibits), and can use armour (unless his faith prohibits) and can cast spells (the ones his faith gives him). He can be the terrible dude in black mail on the black horse with the fiery sword - or he can be the nearsighted monk with surprising strength of will. Or the swamp witch who prays to the fen spirits to take away your blindness. Or something else entirely.