How does character level magic interact with the domain level?
It doesn’t really. Magic-using characters are not assumed to be any more powerful in a combat situation than their more mundane counterparts. Still, a high-level wizard using an adventure action to support a wage war action does have the potential to affect the success chance of the war. He could also make an appearance on the battlefield, perhaps joining with a unit, but a spellcaster would not be any more powerful that a non-spellcaster of the same level.