Preheat the oven to 400°F. In a large mixing bowl, toss the beets with 1 tablespoon of oil. Spread on a large baking sheet lined with parchment paper and bake for 10 minutes. Remove from the oven and set aside.
In the same mixing bowl, toss the squash and peaches with the remaining oil until evenly coated. Mix in with the beets on the baking sheet and sprinkle with thyme (use some whole sprigs and a few loose leaves), salt, and pepper and roast until the veggies are tender and nicely browned, about 10-15 minutes, turning once halfway through.
Meanwhile, in a medium bowl, beat the yogurt with garlic and lemon juice. Season with salt and pepper, to taste. Chill in the refrigerator until ready to use.
Toast the pine nuts in a small pan until golden brown and fragrant. Remove from the heat and let cool. Sprinkle the roasted veggies with the pine nuts and serve with the yogurt sauce.