I don't think that's possible, unfortunately, but it's not GOG's fault. Square-Enix have been selling Thief Gold as part of the Thief Collection, and it's the version they've given GOG to sell, so unless they decide to let GOG sell the Dark Project version as well, you're probably out of luck.

It's likely that the only way to get the original Dark Project version is to buy a used copy of the original disc somewhere.

Having said all that, I hear that the Gold version essentially restores content that was originally intended to be in the game but was cut due to limited time. So it very well could be the "best" version in terms of what the developers intended.