Preheat oven to 400° F.
Cook pasta in a large pot of salted boiling water until al dente, according to package instructions. Drain.
Meanwhile, in a 12-inch cast iron skillet, cook bacon over medium heat until crisp, about 6-8 minutes. Use a slotted spoon to remove the bacon to a paper towel-lined plate, reserving 1 tablespoon of drippings in the pan.
Add the broccoli to the skillet and cook until bright green and heated through, about 2-3 minutes. Remove from the skillet.
Add the butter to the skillet and melt over medium heat. Stir in onion, garlic, thyme and rosemary; cook until the onion is soft, about 5-7 minutes.
Stir in the flour; cook for 2 minutes. Very gradually whisk in the milk; bring to a simmer. Remove the skillet from the heat. Stir in 1 ½ cups of cheddar, salt, pepper and nutmeg until cheese melts. Add cooked pasta, bacon and broccoli; toss to combine. Sprinkle remaining ½ cup of cheddar on top.
Bake until the sauce is bubbly and the cheese is golden brown on top, about 20-25 minutes. Garnish with additional thyme, if desired.