Heat the oven to 400 degrees. Line a rimmed baking pan with aluminum foil and spray with nonstick spray.
Cut the squash lengthwise in half and scoop out seeds. Place the cut side up on the pan; brush with 1 tablespoon of olive oil. Bake for about 1 hour or until the squash is tender but the sides are not collapsing. Remove from the oven and carefully scoop out the flesh to within 3/4-inch of the neck edge. Reduce the oven temperature to 350 degrees.
Meanwhile, in a small saucepan, heat the water and quinoa to boiling, cover and reduce the heat. Cook for 15 to 20 minutes or until the quinoa is tender. Drain any excess water and set aside until ready to use.
In a large skillet, heat the 2 tablespoons oil over medium heat. Cook and stir the onion and garlic in hot oil for 4 to 5 minutes or until softened. Stir in the spinach until wilted. Stir in the mushrooms. Stir in the cooked quinoa, cottage cheese, cranberries, sage, salt and pepper, and chopped pecans.
Divide the mixture between the squash halves. Bake for 10 to 15 minutes longer or until heated through.