By a strict reading of the rules: sure, but he has to pay for it. The market price of a potion is spell level x caster level x 50. The potion maker is free to set the caster level to anything he likes, as long as it's > or = the minimum needed to cast the spell, and < or = his own caster level. So, for a 3rd level cleric with Brew Potion and the Healing domain, a Cure Light Wounds potion can have a caster level between 1 and 4: 1 is the minimum needed to cast the spell, and 4 is the cleric's maximum. If the cleric didn't have the Healing domain, his max caster level for a CLW would be 3. If the cleric decides to make the potion with a higher-than-minimum caster level, it's going to increase the price.
But higher caster levels mean very little to Cure spells. In most cases, +1 caster level gives you +1 point of damage healed - not a big deal. I kind of like the idea of potions made by cleric of a god of healing being a little more potent than those made by cleric of other gods, so I would allow the bonus to apply at no extra cost.