Preheat the oven to 400 degrees Fahrenheit and line a baking sheet with parchment paper. Cut the acorn squash in half lengthwise and scoop out the seeds. Brush the insides with 1 tablespoon olive oil and ⅛ teaspoon salt.
Place the squash halves cut-side-up on the baking sheet and bake for 35-45 minutes, or until it's fork-tender. Remove from heat.
Meanwhile, prepare the quinoa. Rinse quinoa in a fine mesh strainer under running water. Combine quinoa, orange juice, orange zest, and 1½ cups of water in a medium saucepan. Cook on medium heat until it comes to a boil, then reduce heat to simmer. Cook uncovered for 10-15 minutes, or until the liquid is absorbed completely. Turn off the heat and cover the pot with a lid. Let stand for 5 minutes. Fluff quinoa with a fork.
While the acorn squash and quinoa are cooking, heat oil in a medium-large pan over medium heat. Add mushrooms and thyme, and cook for 5 minutes without stirring. Flip mushrooms over and cook for an additional 2-3 minutes. Add garlic, balsamic vinegar, and salt, and cook for 1-2 minutes.
Turn off the heat. Stir in quinoa, cranberries, and the goat cheese.
Add the filling evenly into the acorn squash halves. Garnish with parsley. Serve immediately.