Measure the quinoa into a small saucepan. Cover with cold water, swirl and drain through a fine sieve. Repeat 3 more times. Return rinsed and drained quinoa to the pan, add 3 cups stock, bay leaves, cranberries, raisins and a big pinch of salt. Cover and bring to a boil over high heat. Reduce the heat to low and cook until all the water has been absorbed, about 30 minutes. Turn off the heat and let stand covered 5 minutes. Fluff with a fork. Transfer to a large, shallow bowl, discarding the bay leaves.
Heat 2 tablespoons oil in a large nonstick skillet over medium heat. Add the onions and apples, sprinkle with salt and pepper and sauté until the onions begin to brown, stirring frequently, about 12 minutes. Mix in the allspice and cardamom and stir until fragrant, about 20 seconds. Add to the quinoa. Mix in the 3 tablespoons extra-virgin olive oil and orange zest. Season to taste with salt and pepper. (Can be prepared 1 day ahead. Cool slightly, then cover and refrigerate. To reheat, cover with plastic wrap and microwave in 2 to 3 minute intervals.)
Mix in the parsley and pumpkin seeds and serve.