You mention Halfus, a uniquely Atonement positive fight. Other uniquely Atonement positive fights include Magmaw (if you do the 1 person kiting the worms approach), and the T11 BH boss, who's name eludes me right now. That and Atonement is kind of 5 mans, but who cares about 5 mans.

In fights other than that if you're raid healing then you're just working towards the archangel buff because your raid isn't staying in range of the boss. On fights like Nef you have the larger problem that the tank might not even be in range of the boss because that 15 yards is measured from the middle of the boss, not the edge of his hit box (I REALLY wish they would change that, it would in no way break the game). Atonement is actually in my opinion the superior spec for raid healing, because of Archangel, but you're not using it for the atonement, just the buffs.

The Other Spec, which you should be using if you're tank healing to be honest is the Strength of Soul spec. Where instead of all the Atonement stuff you take some other Raw Throughput, and take Strength of Soul. You're spamming heals on the tank, so their weakened soul dbuff goes away much faster and you keep PW:S on them as often as you can. It's a mana intensive approach, but you're tank healing so PoH is not part of your mana misery, it kind of balances out, and you do get more of your potential maximum rapture procs. So yeah, that's your other option.