Bring a large pot of salted water to a boil and add the spaghetti.  Cook according to manufacturer's’ instructions to al dente.  Just before draining the pasta, scoop out 1 cup of pasta water and reserve.  Drain the pasta, return to the cooking pot and toss with 1 tablespoon of olive oil, cover and keep warm.

While the pasta is cooking, add two tablespoons of olive oil to a large skillet set over medium heat.  Add the sausage links and cook, turning to brown them on all sides, about 8-10 minutes.  Remove from the skillet to a plate and reserve.

Add the chopped onion and garlic to the accumulated fat in the skillet and cook until the onion is soft, 3-4 minutes.

Stir in the butternut pasta sauce, red pepper flakes, cumin, lemon juice, salt and pepper.  Cook over medium heat, adding reserved pasta water in 1/4 cup portions until the sauce thins out enough that it stops sputtering. Stir in the butter and the thyme leaves.  Add the drained pasta, tossing to coat evenly. 

Divide the pasta into shallow pasta bowls and add a sausage link to each serving.  Garnish with additional thyme leaves and thyme sprigs.  Serve immediately