Heat 2 tablespoons oil in a large cast-iron skillet over medium heat. Add chopped onion and 3 thyme sprigs; cook, stirring occasionally, until softened, 5 to 7 minutes. Add 2 tablespoons minced garlic, ¼ teaspoon plus ⅛ teaspoon salt and ¼ teaspoon crushed red pepper; cook, stirring often, until fragrant, about 1 minute.
Stir in 3 cups vegetable broth, 1 teaspoon lemon zest and 1 tablespoon lemon juice; bring to a boil over medium-high heat. Add rinsed beans; cook, stirring occasionally, until heated through, about 2 minutes.
Divide the beans and broth among 4 bowls. Sprinkle with ¼ cup Parmesan. Garnish with crushed red pepper and/or lemon zest, if desired. Serve with toasted baguette.
