Melt butter in a large soup pot over medium heat, then add sliced onion, Kosher salt, and sugar. Stir well, then cover and cook. Remove the lid, then continue cooking until the onions are uniformly caramelized.
Increase the heat to medium-high, then pour in 1 cup red wine, being sure to scrape the bottom of the pan to release any browned bits. Cook. Pour in low-sodium chicken stock, then add thyme sprigs, bay leaves, remaining Kosher salt, and freshly ground black pepper. Bring to a boil.
Preheat an oven. Place baguette cubes on a rimmed baking sheet lined with parchment or foil, then drizzle with olive oil and a little Kosher salt. Bake until crispy. Remove and set aside.
Discard the thyme and bay leaves, then ladle the soup into individual serving bowls placed on a rimmed baking sheet. Top with as many croutons as you like between the bowls and sprinkle on top. Cool slightly, then serve immediately!