Makes 40, serves 8 to 10
Preheat oven to 400°F. Line a baking sheet with parchment paper. With a paring knife, carefully remove the stems from the mushroom caps. Finely chop the stems and set aside. Toss the mushroom caps with 2 tablespoons of the oil and place cup side-up on the baking sheet. Season with salt and pepper.
Add 1 tablespoon of the oil to a medium sauté pan and heat over medium heat. Add the sausage and sauté, breaking it up with a spatula, until the meat is cooked through, transfer to a medium mixing bowl and set aside.
Add the remaining tablespoon of oil and heat over medium heat until hot. Add the chopped mushroom stems, onion, red pepper, and thyme and sauté until the onion is translucent, 8 minutes. Add the freekeh and stir to coat the grains with the vegetables and oil. Add the broth, bring to a boil, and reduce heat to low. Cover and simmer gently until the grains are tender and have absorbed all the broth, 20 minutes.
Pour the freekeh into the bowl with the sausage. Add the cheese and parsley and season to taste with salt and pepper. Generously stuff the mushrooms with the freekeh mixture. (The mushrooms can be made up to this point and refrigerated, covered, for up to 8 hours.) Bake the mushrooms for 20 to 25 minutes, adding 10 minutes cooking time if the mushrooms have been refrigerated. Serve warm.