I'm making this post to present an argument as to why this system is broken and needs fixing, preferably sooner than 5.1, and my suggestion as to how it can be fixed. If they could hotfix it next Tuesday that'd be my choice.
As I see it, there are two big problems that are good evidence that motes and spirits shouldn't be BoP.
1) Crafters don't gather mats themselves. In a way, having an auction house helps exacerbate this, as you're creating a tiered production model where people can make a lot of gold whether they're controlling resource production, material production, or goods production. Whether crafting for themselves or for others, crafters buy mats from the AH, they don't farm them. I'm sure there's a minority of people who do, but I have dedicated farmer alts that I use to help supplement my supplies when the AH runs low.
The Point: I play a lot on my main toon, and even there I'm starved for motes. When I can grind through all of the level 90 daily quests and I can't make enough in a week to make due? That's a problem.
2) This feature is a great way to get crafters to stop crafting items. Spirits of harmony are required to purchase a great many recipes and craft a great many items, but you'll notice that they're completely absent from enchanting. That's because attaching spirits to the enchanting profession would kill any coherent enchanting strategy for the game. The same can be said of jewelcrafting, as stopping people from learning gem cuts would be insane. The only serious obstacle I see is that spirits are required for the leg armors, which means that market is going to stay strong and extremely valuable.
The Point: Who wants to spend two spirits of harmony to craft a level 415 blue weapon that you'll replace in a heroic dungeon? This feature means that there's no reason to craft leveling gear.
My suggestion is pretty simple. Make spirits non-BoP. That way people still have to gather motes, but a market can spring up around selling spirits. And given that motes are fairly hard to get, spirits will still end up being quite valuable.