Toss the butternut squash cubes and onion pieces with 1 tablespoon of olive oil. Spread them out evenly on a baking sheet. Roast the vegetables for 20 to 30 minutes at 425 F or until fork-tender.
About 5 minutes before butternut squash and onion are done, heat the other tablespoon of olive oil over medium heat in a stock pot. Add the diced carrot and let it cook, stirring occasionally, until it starts to soften, about 5 minutes. Add the garlic, roasted butternut squash, roasted onion, diced tomatoes and the juice and vegetable stock. Stir well and then add the cannellini beans, sage and thyme leaves.
Bring the soup to a simmer and let it all cook together for 15 to 20 minutes.
Once the soup has simmered, remove it from the heat and puree it using either an immersion blender or a stand blender.
Stir in the apple cider vinegar, and then add the heavy cream.