Since when is the point of healing to have high HPS? Is it some kind of competition with your group's other healer(s)?
Atonement is very good as a kind of sparse AoE heal, and overhealing from atonement is extremely low. But atonement has no throughput. If you're in an encounter where you need to heal balls out then atonement is not the answer; spirit shell and cooldowns are. If you're in an encounter where by and large the healers aren't stressed, then atonement is probably what you should be doing. The fun of disc (and MW) is that you have that option.