I don't want to read that whole thread, but it seems like they're talking about specs for specific bosses and 10-mans. I talk about things from a more general standpoint a lot of the time, and I do have a 25-man bias that I unfortunately, thanks to blizzard, cannot remedy. That said, you have to determine what's best for you based on the needs of your raid. Don't take my word for it, don't take Jhazrun's word for it, sometimes you have to think for yourself. You might not be sure of your decision at first but feel it out and see. The confidence comes with time.

That said, I explain the weakness of Atonement vs. SoS in this post http://wow.joystiq.com/2011/05/02/spiritual-guidance-the-aftermath-of-patch-4-1-for-holy-and-disc/

SoS throughput is very sustainable, unlike what Jhazrun says. He didn't mention Heal at all, and it's unfortunate that so many priests ignore it when it's incredibly versatile. You have to use it strategically with borrowed time and such.

But like I said, there is room for disagreement. Keep in mind that there are tons of top priests in the US who don't and won't take Atonement. The numbers on it are pretty terrible but as a utility/filler it is viable.