Preheat the oven to 375°F (190°C).
Cook the whole wheat elbow macaroni according to package instructions until al dente. Drain and set aside.
In a large skillet, heat olive oil over medium heat. Add the chopped onion and sliced mushrooms and sauté for 5 minutes until softened.
Add the minced garlic and cook for 1 minute until fragrant.
Sprinkle the flour over the vegetables and stir well to coat. Cook for 1 minute to remove the raw flour taste.
Gradually whisk in the lowfat milk, stirring constantly to avoid lumps. Cook until the sauce thickens, about 3-4 minutes.
Remove the skillet from heat and stir in the lowfat cottage cheese, Greek yogurt, Dijon mustard, dried thyme, and black pepper until smooth and well combined.
In a large mixing bowl, combine the cooked macaroni, drained tuna, thawed peas, and the prepared sauce mixture. Stir gently to combine.
Transfer the mixture to a greased 9×13-inch baking dish.
Sprinkle the shredded reduced-fat cheddar cheese evenly over the top.
In a small bowl, mix the whole wheat breadcrumbs with a little olive oil to lightly coat them, then sprinkle evenly over the cheese layer.
Bake uncovered for 20-25 minutes, or until the casserole is bubbly and the topping is golden brown.
Remove from the oven and let it cool for 5 minutes before serving.