Without wiping out the pan, reduce the skillet heat to medium. Add the remaining tablespoon of oil, swirl to coat the pan, then add the red onion and let cook until slightly softened, about 3 minutes, scraping the browned bits off the bottom of the pan as it cooks. Add the garlic and let cook 30 seconds, just until fragrant. Add the tomatoes, thyme, and remaining 1 tablespoon balsamic vinegar, 1 teaspoon honey, ½ teaspoon salt, and ¼teaspoon pepper. Increase the heat back to medium high and cook until the tomatoes begin to soften slightly, about 2 minutes.