Well, for Legion, Atonement will be the primary healing method for Disc Priests, so it'll be interesting to see how it turns out, and how well the balancing is done on it. It is quite different from the old system in it's chore though.

Currently, from what I've read it's going to work so that you first have to choose your atonement target(s) by casting specific spells on them (Power Word: Shield, Shadow Mend, Power Word: Radiance), and then any damage done heals ALL* atonement targets for 40% (before factoring mastery) of the damage done. The main difference obviously is that the automatic smart healing is gone. Now, I doubt it'll be too hard to come up with a rotation that gives your toons atonement from atleast a few of the priests at all times, but it still poses new challenges.

* based on current tooltips.

The balancing side of the spec is going to be interesting to say the least. Due to the slow 2-step mechanism and the conversion rate of DPS to Healing, I would say that it's likely that Discs are now a more or less AOE raid healers (old resto Durds anyone?). It would appear that their healing scales rather well as the number of atonement targets increases. Additionally it's worth noting that if the damage they can do while keeping up with other healers is at all significant (maybe even 20% of a normal DPS) I don't see how they are not an auto-include to most progression raid groups. All in all, fascinating to see how it turns out.