I do it with a couple of altered classes and prestige classes.
1. Set Allow Class Abilities to Cleric. This will inherit its custom abilities, which are domains.
2. Add one to the cCustTot field on the class.
Code:
field[cCustTot].arrayvalue[0] += 1
3. If you want the class to have additional domain spells per level.
Code:
field[cSecSplReq].value += 1
I believe this is all you have to do to get it to work. Not entirely sure though, I'm just looking at my setup. It may have some other underpinnings I'm not aware of, but nothing jumps out at me.