Adjust oven rack to upper middle position and preheat oven to 375 degrees F. Coat squash halves with 2 tablespoons olive oil and season with salt and pepper. Place on a rimmed baking sheet lined with aluminum foil with cut side facing up. Place garlic clove and thyme sprig in each seed hollow. Roast until completely tender and lightly browned in spots, about 1 hour total. Remove from oven and allow to cool slightly. Discard thyme and carefully scrape flesh away from skin. Discard skin.