In a medium bowl mix the tomatoes with ½ teaspoon oil and a pinch of salt. Brush the eggplant, zucchini, and onion slices on both sides with oil and season evenly with salt, pepper, and ½ teaspoon of the thyme.
Prepare the grill for direct cooking over medium heat (350° to 450°F) and preheat a perforated grill pan for 10 minutes.
Brush the cooking grates clean. Grill the eggplant, zucchini, and onion slices on the cooking grates over direct medium heat, with the lid closed, until marked and tender, 10 to 12 minutes for the onion and 8 minutes for the eggplant and zucchini, turning once or twice. At the same time, grill the tomatoes on the grill pan until warmed and lightly marked, 3 to 5 minutes. Remove the vegetables from the grill and let rest until cool enough to handle.
In a large bowl whisk the vinegar, 1-½ tablespoons of the basil, the garlic, and the remaining ½ teaspoon thyme. Slowly whisk in 5 tablespoons oil. Season with salt and pepper.
Chop the eggplant, zucchini, and onion into ½-inch dice. Place in the large bowl with the dressing and add the beans. Gently fold in the tomatoes and garnish the salad with the remaining basil. Serve warm or at room temperature.