Newest changes to the Public Test Realm show that the Atonement nerf has been lessened. Previously healing caused by dealing holy damage to heal a nearby target by 100% then it was nerfed to 80% and now it is up to 90%. Personally I think it was just fine at 80% when you take advantage of Grace, which increases healing received and stacks 3 times, penance makes it dirt simple to apply 3 stacks whenever you want.
I personally use atonement all the time and I came to the following conclusion: atonement was overpowered and dissevered a nerf--- I mean correction, yes, the skill needed a correction. In my opinion it should never be better than regular healing. Well, it works just fine in Heroic Dungeons and I've seen videos of it being used in Raids.
We'll see later on how this turns out.