In a large skillet add the butter and red onion. Saute until slightly soft, about 1-2 minutes.
Next add in the garlic, saute for 30 seconds, stir and add the butternut squash, chicken stock, sage, and thyme. Stir and cover. Cook until the butternut squash is fork tender, about 8-10 minutes.
When the squash is tender, add the squash to a food processor along with the milk and salt to taste. Puree until smooth.
In the meantime heat a small skillet to medium high heat, add the diced bacon to the pan and saute until the bacon is crispy. About 4-5 minutes. When the bacon is done, place it on a paper towel lined plate to let the grease drain.
Bring a large pot of water to a boil. Add gluten free pasta, cook according to directions, (6-8 minutes) do not overcook.
Drain pasta and add butternut squash sauce to the pasta, gently toss together and top with crispy bacon. Serve!