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Butter a 2 ½ quart casserole. Melt 5 tablespoons butter in a medium saucepan over medium heat. Whisk in flour, stirring until smooth; cook 1 minute. Slowly whisk in about ½ cup of milk, stirring until no lumps remain; whisk in remaining milk and salt.
Increase heat to medium high and cook, whisking constantly, until milk mixture thickens and large bubbles break at the edges of pan. Reduce heat to low and whisk in cheeses, stirring until they are completely melted and sauce is smooth; cover and keep warm.
Heat oven to 350 degrees. Bring a large pot of salted water to a boil and cook macaroni for 3 minutes fewer than the package instructions; drain well. Add macaroni to cheese sauce (be sure your pot is large enough to contain both the pasta and sauce); mix well. Transfer macaroni to prepared casserole.
In a small bowl, toss cherry tomatoes and thyme with a teaspoon of olive oil; season with a pinch of salt and pepper. Sprinkle tomatoes over surface of macaroni and cheese. Bake for 15 minutes, then toss breadcrumbs with remaining teaspoon of olive oil and sprinkle over tomatoes. Bake 15 minutes more, or until edges are bubbling and golden and breadcrumbs are toasted. Wait 5 minutes before serving.