Bring a large pot of heavily salted water to a boil. Cook the penne according to the package directions. Reserve 1 cup of the starchy pasta water, drain the penne, rinse with hot water, and reserve.
While the pasta water is boiling, heat the olive oil in a large skillet over medium-high heat. Add the onion and cook until tender, about 5 minutes. Add the garlic and red pepper if using and cook for another 30 seconds. Add the kale and cook, stirring, until tender, about 3 minutes. Add the vegetable broth, pumpkin puree, cinnamon, nutmeg, yeast, and vinegar, and stir until heated through, about 5 minutes.
Add the drained pasta to the sauce, stir and add in some of the reserved pasta water to thin the sauce a bit. Taste and adjust seasoning with more salt and pepper if needed. Cook until everything is heated through and serve with pumpkin seeds.