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Looking through my old Player's Guide to Kalamar, I hit upon a mechanic that could be "borrowed" and make backwards compatibility with Domains work.
In Kalamar, a cleric can take a feat that allows them to expend a Channnel Energy based on their domains. Getting rid of the idea of it costing a feat, I think that a thematic (based on Domain) option for Channel Energy could replace the touch-based attack at 1st level. This ability would be a choice; a cleric could expend a use of Channel Energy for the effect or use it as normal.
Example:
Air Fire, Earth, Water Domains
Elemental Barrier (Su)
A cleric with the appropriate Domain (Air, Fire, Earth, or Water) can choose to expend a use of his Channel Energy, providing the cleric and every ally within 30-ft. radius with Resistance 10 to the appropriate element fpor a number of rounds equal to his cleric level + his WIS modifier.
I know this is probably more work and that it needs clarification, but an option for this or the SRD Domain power could be chosen at 1st level. And expandng this to allow a choice between this, the touch-based attack or the SRD ability gives the players options for customizing.
Just a thoguht.