What I'm saying here is not based on experience, it is based on stated deisgn goals amalgamated from both Cataclysm and MoP betas, the PTR discussions, GC's statements on the forums and in tweets, and conversations here on this very forum.
The separation between design goals and your experience is, sadly, the worst failing of the Discipline spec; it is not being realized even close to what it is intended and also tends to exist outside of the grander 'healing' vision, which leads to the 'your heals are weak because you have absorbs'. The players keep finding ways of kludging it together, which invariably ends up in loops of nerfs and buffs just to balance the numbers, regardless of the actual cohesion.
As for Atonement killing the concept behind the intended use of "always be casting", it started with Heal and has since gone on a huge arc of eating other intended spells, much like PoH. On the PTR, Atonement with the recently buffed Penance has almost taken the place of the currently bloated PoH in that it is almost the best answer to everything. While Atonement isn't solely responsible for the death of the 3-heal model and meaningful spell decisions, it certainly didn't help. Like anything else, the idea has to be maintained and sadly it hasn't. Not that it was all that popular or effective anyway, but they do need to either stick to it or replace it with something else instead of letting it rot away. It was the foundation on which all pre-MoP healers was built and if they let it erode as it has, it's no wonder that so many of the healing specs are having issues with balance.
See, again I tend to wander and probably poorly express what I mean. My old writing professor is probably rolling in his grave. -.-
Nope, it was very clear (and interesting!)--thank you.