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 chopped onion and cook for 3-4 minutes until softened.
Add minced garlic and chopped mushrooms to the skillet and cook for another 4-5 minutes until mushrooms are tender.
Sprinkle the flour over the vegetables in the skillet and stir well to coat. Cook for 1 minute to remove the raw flour taste.
Gradually whisk in the lowfat milk and continue stirring until the mixture thickens, about 3-4 minutes.
Remove the skillet from heat and stir in the lowfat Greek yogurt, Dijon mustard, dried thyme, salt, and black pepper until smooth.
In a large mixing bowl, combine the cooked macaroni, drained tuna, thawed peas, and the sauce from the skillet. Mix gently to combine.
Transfer the mixture to a 9×13 inch baking dish. Sprinkle shredded reduced-fat cheddar cheese evenly over the top.
Sprinkle whole wheat breadcrumbs evenly over the cheese layer.
Bake uncovered in the preheated oven 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.