In a skillet over medium heat, cook pancetta until crispy, about 8 to 10 minutes. Remove pancetta with a slotted spoon. Pour off all but 2 tbsp of the pancetta fat. Stir onion into same pan and sauté 4 to 5 minutes over medium heat until softened. Add garlic and red pepper flakes; cook 2 minutes. Stir in tomatoes, 2 tbsp of the cheese, the thyme and cooked pancetta. Bring to a simmer and cook 10 minutes.