It's probably best like you say, use em, sell em or they're gone.
This has got the disadvantage of completely reshaping ye ole EoFS economy. You'd have to come up with some new balance to accomodate it.
I have a vague recollection of discussing this half-baked idea on the EoI forum, where the economy would work as stated above, with only production potentials and no stockpiles.
The conclusion, I believe, was that trade with the guild would need to play a major role in the game. Otherwise losing a few cities could irrevocably cripple you with little hope of catching up with the rest of the players.
So it went like this: houses automatically offer their surplus production on the guild-controlled market(with the option to opt out), and whenever any house wants to buy something, they make use of that surplus. There's only as much stuff to buy as is produced by other houses. Since the guild is controlling the trade, the price houses sell at is lower than the price to buy the same stuff. The difference going to the guild coffers, which may or may not have other uses.
One could bribe the guild to embargo a house(no access to the market), or to rise prices on some stuff.
It would pretty much require universal warehouse(i.e., pooled production capacity per house, rather than per planet), which may not be such a bad idea, considering the intended lack of meaningful fleet operations, so no military blockades. Also, further simplification, which is good.