Bring a large pot of water to a boil and salt generously until it tastes like the ocean. Add pasta and cook until al dente, according to package instructions.
Melt butter in a large pot over medium heat. Add onion and cook until soft and translucent, about 10 minutes. Add garlic and cook until fragrant, 1-2 minutes, then add flour and cook another minute, stirring constantly. Gradually whisk in the milk and bring to a simmer. When you notice sauce has thickened a bit, whisk in the pumpkin and salt. Bring back up to a simmer then reduce heat to low and stir in the parmesan. Taste and add more salt as needed.
Heat about 1/2" oil in a small saucepan over medium-high heat. When shimmering hot, carefully add sage leaves. Cook until crisp and starting to brown, a minute or two.
Drain pasta and return to pot. Add sauce and toss to coat. Top individual bowls with a sprinkling of parmesan, some crumbled crispy sage, an a sprinkle of red pepper flakes, if desired.