In heavy saucepan, heat oil over moderate heat and cook onions, salt and garlic until tender and starting to color, stirring several times. Add flour and stir while cooking for a minute. Add tomatoes, salt, pepper, stock and basil, and simmer for 20 minutes.Process to a creamy texture. You can use an immersion blender, food processor, or traditional blender for this step. Finish with orange zest and thyme leaves, and serve.