Spray a large pot with olive oil and add onion and apple. Cook until the apple is soft, about 8 to 10 minutes. Add quinoa, broth, apple juice, thyme, crushed red pepper, salt and pepper and bring to a simmer. Cover and cook for 10 minutes. Add all but 1/4 cup of the cheese and cook over low until melted. Allow to cool slightly then working in batches, puree in a blender.
Meanwhile, preheat the broiler. Spread mustard on bread and top with remaining cheese. Cook until cheese is melted and then cut into 1” squares.
Ladle soup into bowls and then top with croutons and chives.