Disc priest have done exceptionally well in WOTLK and CATA without atonement.
Disc in Wrath had ridiculously OP bubblespam.
Disc in Cata had infinite mana and auto-DA on PoH.
This is actually the first time in three expansions that Disc has not been essentially a one-button spec. Believe it or not, the current Spirit Shell/Atonement/PWS game is actually a step up in complexity and a step down in power from where Disc has been for the last five years.
Are they still frustrating to play with? Yes. I play a holy priest (well, one and a half holy priests, actually) in raids with disc priests. Believe me, I have every reason in the world to want Disc balanced. But first of all, they're not that imbalanced, and secondly, your proposed solution would break the spec.
And there isn't a good solution. Or, rather, there aren't any good solutions that Blizzard would actually implement, because they're married to Grace and Chakra. So we might as well all shut up, because the current balance (minus the small nerfs we're seeing in 5.3) is about as good as it's going to get. The only other thing I can think of is nerfing Rapture.
Any more major nerf will set the balance pendulum in motion again, and that's never good. The first reaction tends to be buffing PoH. By a lot.