Preheat the oven to 425. In a small bowl, mix the parsley and lemon zest by gently tossing them with your hands until combined. Set aside.
On a sheet pan or in a large baking dish, toss the cherry tomatoes with ¼ cup of olive oil and thyme. Season generously with salt and pepper. Roast the tomatoes for 20 to 25 minutes, until they have collapsed and start to turn golden around the edges. While the tomatoes finish roasting, heat 2 tablespoons of olive oil in a large (12-inch) skillet or Dutch oven over medium heat. Add the onion, garlic, and red-pepper flakes, cooking for 4 to 5 minutes until the onion softens and the garlic becomes fragrant. Stir in the rinsed beans and broth, and bring to a simmer. Gently mash about ½ cup of the beans with a spoon to thicken the broth slightly. For a thicker stew, mash more beans. Season with salt and pepper.
Once the tomatoes are done roasting, add them and their juices to the stew. Simmer for another 5 to 10 minutes to meld the flavors, then adjust seasoning with more salt if needed.
Ladle the stew into shallow bowls. Top with the lemon-parsley mixture and drizzle with extra olive oil. Sprinkle with flaky salt if desired, and serve with toasted bread on the side.