Peel the butternut squash. You can follow this method: score the butternut squash superficially with a fork and place it in the microve. Microwave on high for about 6 minutes, turning every 2 minutes or so. Remove from the microwave. When cool enough to handle, peel it. Cut in half transversally, then cut each piece in half lengthwise. Remove the seeds and fibers with a spoon.
Slice the butternut squash portions in wedges and place in a bowl. Add the whole garlic cloves (peeled or unpeeled), 2 Tbs olive oil and 3 or 4 branches of thyme and mix to coat every slice of squash and clove of garlic
Line a cookie sheet with parchment paper and spread the squash wedges, thyme and garlic cloves. Bake for 40-50 minutes until soft and golden, adding a bit more water if the pieces start to brown.
While the squash is in the oven, slice the onion and sauté it in 2 Tbs olive oil.
When the squash is done, place it in a stock pot. Peel the garlic cloves and place them in the pot. Discard the thyme. Add the onion and 2 cups stock. Add the cumin and stir to mix. Blend with an immersion blender, adding more stock as necessary for the desired thickness (alternatively, you can use a blender, working in batches). Season with salt and pepper.
Serve hot, garnishing with a drizzle of extra virgin olive oil and a small branch of thyme.