Place roasted beets, olive oil, balsamic vinegar, wine, garlic, 1/4 cup of the Parmesan, and a little salt and pepper in a food processor. Pulse until it’s smooth.
Transfer beet mixture to a small saucepan. Add the stock, cream, and thyme sprigs; bring to a light simmer.
Add the sugar, remaining cheese and another pinch of salt. Simmer on low while your pasta cooks.
Cook the penne until al dente (about 11 minutes.) Drain and return to pot. Discard thyme from the sauce and pour over the pasta; toss to combine. Season accordingly.
Serve in bowls, sprinkle with grated Parmesan and garnish with a thyme sprig or two.