Rinse quinoa in a strainer. In a heavy-bottomed saucepan, bring quinoa, 2 cups water, and 1/4 tsp salt to a boil. Cover, reduce heat and simmer until quinoa absorbs the water, about 12 to 15 minutes. Meanwhile, heat oil in a large skillet over medium-low heat. Add onion; cook until translucent, about 5 minutes. Raise heat to medium-high and add garlic, zucchini, carrots, thyme or oregano (if using), and red pepper flakes. Saute, stirring frequently until vegetables are tender and gold at the edges for about 8 to 10 minutes. Season with remaining salt and black pepper. In a large bowl, mix together quinoa, vegetables, fresh chives and serve.