Position oven rack 5 inches from broiler; preheat to 350°F. Lightly coat a 13-by-9-inch broiler-safe baking dish with cooking spray. Combine water, quinoa, oil and ¼ teaspoon salt in a large saucepan; bring to a boil over medium-high heat. Reduce heat to medium-low; cover and cook, undisturbed, for 10 minutes. Add broccoli to the mixture (do not stir); cover and continue cooking until all the water is absorbed, about 5 minutes. Remove from heat; let stand, covered, for 5 minutes.
Transfer the quinoa mixture to a large bowl. Add beans, milk, yogurt, thyme, garlic, pepper, onion powder, 1 ½ cups cheese and the remaining ¼ teaspoon salt. Gently stir until evenly combined. Spoon the mixture into the prepared baking dish. Sprinkle with the remaining ½ cup cheese.
Bake until heated through and the cheese is melted, about 15 minutes. Set oven to broil (without removing the dish). Broil until lightly browned, about 3 minutes. Remove from oven; let cool for 5 minutes. Garnish with additional thyme, if desired.
