Currently there is a cooldown, and there is a cooldown on the current test realm build.
So, it will probably remain in the game for a while.

I see the removal of cooldowns, as a method to allow crafting to gear toons to a point where they can raid.
The same as heroic badges are currently.
But enchants/gems aren't so much gearing, as they are the final additions to gear (tweaking).

However, even if cooldowns are removed for the remainder of this expansion.
There will be a cooldown on the transmutes (epic gems, cloth, ore etc) for most of Cataclysm.
So in that eventuality, then we're just getting our toons into a position to make the killing in Cataclysm instead of now and in Cataclysm.