Originally, we did exactly that IMC. We let people swap for any of their domain spells, instead of cure/inflict.
There was a problem as time went on. It's just a bit too strong. Let's say I took two non-healing domains, and then loaded up every slot with heal spells. I'd be like a Sorcerer who knew three spells at every level, immediately upon reaching that spell level, one level earlier than normal. Not counting my better BAB, HP, turn undead, granted powers... oh, but no familiar.
It's also just a lot stronger in general. Let's say a person picks Healing as one of their domains. Besides having the option of swapping for a non-healing spell, this Cleric would be much stronger since he could swap for Heal instead of being forced to use Empowered Cure Critical Wounds. Swapping every high-level spell for Mass Heal would do the same.
If the person only has two domains, it's not a big deal and can be compensated for in other ways. If the person takes PrCs to where they have a half-dozen domains, then it's REALLY unbalanced. They become better spontaneous spellcasters than Sorcerers; even if they loaded every slot with the same spell, that'd still be like a Sorcerer knowing N+1 spells at each level.
One solution would be to drop all Clerics to one domain. The better solution, IMHO, would be to say that you can swap for whichever domain spell you selected for that level that day. You know, in that extra non-swappable domain slot. So, you still only have one option when you spontaneously cast, but now you have the added flexibility of picking each day, AND you're less healing-oriented.
Oh, and you also need to say that Clerics can't metamagic a spontaneously cast spell at all. If you want it metamagicked, put it in the domain slot that way.