Preheat the oven to 400°F (200°C).
In a medium bowl, toss the sliced Roma tomatoes with the turkey pepperoni, olive oil, 1 teaspoon Italian seasoning, and 1/2 teaspoon garlic salt; add a pinch of black pepper.
Spread the tomato and pepperoni mixture in a single layer on a baking sheet and bake until tomatoes soften, about 13–15 minutes; remove pepperoni early if it crisps in 6–7 minutes and continue roasting tomatoes until tender.
While the tomatoes roast, bring a large pot of salted water to a boil and cook the gluten-free macaroni according to package directions; reserve 1/2 cup of the pasta cooking water, then drain the pasta.
Return the drained pasta to the pot, stir in 1/3 cup of the reserved pasta water, then add the grated mozzarella and Parmesan a little at a time, stirring until each addition melts and creates a smooth cheese sauce.
Stir in the 1/2 cup Greek yogurt until the sauce is creamy. Add the remaining 1 teaspoon garlic salt and 1 teaspoon Italian seasoning, and season with a pinch of black pepper; if the sauce is too thick, add the remaining reserved pasta water to reach the desired consistency.
Fold the roasted tomatoes and crisped pepperoni into the mac and cheese until evenly combined, then serve immediately.