Option 1 : You don't need to sell it at 2g/u because you've make your money with the other products of shuffling. (essence, rare gems...)
=> At 2g/u it's better to stockpile for wow 5.0 where many people will need the dust to level.
For exemple Infinite Dust is now at 100-150g per stack on many server.
Option 2 : You need to sell at 2g/u to turn even.
=> Stop the shuffling and go to greener pasture.
Option 3 : You make too many dust from green gems : Switch to Speculation on Fire Prism so stockpile the greens to make many of them. (Too bad it also use a carnelian...).
Option 4 : Reduce the numbers of color that you shuffle, sells or stockpile for later in this expansion or for 5.0 purple and orange colors for the JC and Alchi that need to level their profession.
I've picked orange and purple cause it's the most used after red. If when epic gems appears the BIS is to gem orange on many slots, it's easy to transmute to rare version of orange and to sell or transmute to epic version next. For the purple it's a little harder due to the price of the Jasmin.
Option 5 : bags, scroll that consumes the dust ( scroll at 8g for 12 dust...).
Nissaya hit the nail on the head. Only thing I would add is to look out for insanely cheap herbs and potentially use them to transmute the green gems instead of turning them into dust.
At the moment the only green quality gems that I end up turning into dust are the jaspers. Most of the rest I transmute and sell as cut gems. But my realm may be abnormal in that the price of ore has stayed rather high and the price of herbs has crashed.