Preheat oven to 450º F. Spray a baking sheet with cooking spray or cover with parchment paper.
Cut the peppers in half lengthwise, leaving stems on. Carefully remove seeds. Place peppers, cut-side down, on the baking sheet. Bake for 10 to 15 minutes, or until just tender. Dice 2 halves; set all peppers aside.
While the peppers are baking, rinse the quinoa. This step is necessary to remove the bitter natural saponin coating of the quinoa kernel. Combine quinoa, water, and salt in a medium saucepan and simmer, covered, until tender, 10 to 15 minutes. Set aside.
Toast pine nuts in a dry skillet over medium heat, about 5 minutes, stirring, until lightly browned. Remove from skillet and set aside.
Over medium heat, warm the oil, then sauté the scallions and cumin for about 2 minutes until softened. Add Swiss chard and cook, stirring occasionally, for 2 to 3 minutes, until greens are wilted. Remove from heat. Stir in cilantro, parsley, dill, lemon juice, lemon zest, reserved chopped pepper, cooked quinoa, and pine nuts. Adjust seasoning with salt and pepper.
Spoon the mixture evenly among pepper halves. Serve warm or at room temperature.