I remember that a ways into 3.5e, the Forgotten Realms introduced Initiate feats, which gave you a bonus and access to a list of spells exclusive to that particular faith. Perhaps something along those lines would be useful. You would come up with some faith-appropriate benefit for the feat and then develop a list of prayers only for those clerics with that feat. Might not be worth it, but if you'd prefer something like the domains, I would try that and the creation of the various Channel Divinity feats, as suggested above.