For the salad: Bring a large pot of salted water to a boil over high heat. Add the pasta and cook until tender but still firm to the bite, stirring occasionally, about 8 to 10 minutes. Drain and place in a large serving bowl. In a medium saucepan, heat the oil over medium-high heat. Add the onions and season with a pinch of salt and pepper. Cook, stirring occasionally until golden and tender, about 10 minutes. Add the garlic and cook for 30 seconds until aromatic. Add the broccoli and saute for 1 minute. Add the water and scrape up the brown bits that cling to the bottom of the pan with a wooden spoon. Cover the pan and cook until the broccoli is tender, about 4 minutes. Add the beans and cook for 1 minute until warmed through. Transfer the onion mixture to the serving bowl. Add the Parmesan cheese and toss with the fregola.
For the dressing: In a small bowl, combine the lemon zest, lemon juice, olive oil, honey, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Whisk until smooth. Stir in the chives.
Pour the dressing over the fregola and toss well until coated. Season with the remaining 3 teaspoons of salt and 1 teaspoon pepper and serve.