In a large saucepan, heat the olive oil. Add the wheat berries and cook over moderate heat, stirring, until lightly toasted; the grains will turn slightly opaque just before browning. Add the onion and thyme and cook over low heat, stirring, until the onion is softened, about 5 minutes. Add the water and 1 teaspoon of kosher salt and bring to a boil. Cover and cook over very low heat until the water is absorbed and the grains are tender. Fluff the grains and discard the thyme sprigs. Season the grains with salt and serve.
The cooked grains can be refrigerated for up to 5 days or frozen for up to 1 month.