Nerfing the healing done from atonement means that Spirit Shell, Prayer of Healing, Prayer of Mending, Power Word: Shield, et al are all untouched. It means when you push archangel because you need to heal harder, that you still can and in doing so will be unphased completely, but your ability to stand at max range and spam a basic dps rotation with little regard to actual healing patterns is no longer supported.
As pointed out, Atonement at one point in time replaced Heal. That's it. Not Flash Heal, not Greater Heal. Just Heal. At this point, with it being a top heal on most fights, it's pushed a few too many boundaries. Sure you could say it's "three spells", but given that the other spells are rotationally cast on cooldown and that all three spells are all smart heals using the exact same mechanic, I would like to call butts on that.
Atonement nerf: Needed. Doesn't affect Discipline's PvP offensive burst, or its burst healing, cooldown usage, or actual utility when using "real" healing spells. If you want to spam dps spells on a boss all day long, and nothing else, roll a mage?