It looks like things scale from one or the other, not exclusively SP (reference Exo).
From the new Beta build information on MMO-C (build 15640), it seems that every ability will scale from SP alone and not from AP (directly, anyways).
I think this is just some (belated) cleanup in design. Ret Spellpower wasn't just AP/2 due to all-stats enchants and raid buffs like Kings/MoW. Holy AP wasn't just their base value for the same reasons. It produces some (rather small) double-dipping. MoP would just exacerbate this as stat bonuses are seeing another big leap.
Instead of just assuming Holy have zero AP buffed and Ret have zero SP buffed (before AP->SP conversion), it looks like they're taking the simple route: Build a spell to function solely on one of the two values (SP or AP, never both). They can then always know that Ret SP = AP/2 and Holy AP = baseline. I'd suspect that makes intended damage easier to balance. Produces a minor reduction in chance of wild buff/nerf cycles, and probably makes Holy soloing (especially leveling) easier to set precisely where they desire.
Regarding HoW - it looks like the intent is to remove HP from it. I'm thinking either it's still intended for use under AW (or Sanctified Wrath is pointless above 20%?!?), or SW is to be updated (hope so, I've constantly worried about SW's PvP impact). It may be designed as a non-RNG-based, under-20%, rotation changer. Produce enough damage to be desirable even before (some? all?) HP generators and you'd want to work it into your priority, but you couldn't use it all fight long. If that's the goal, I like the idea since it would alter priority on the fly (at 20%) without being the RNG rollercoaster or procs. However, in order for this to work the total damage done must average more than at least some of our HP generators (+1/3 of the TV they then don't produce). That always has PvP spike implications, especially in a sub-20% scenario.