Melt the butter in a medium pot over medium heat. Add the onion and cook, stirring occasionally, until softened, about 5 minutes. Add the garlic and thyme and cook, stirring, until the garlic is fragrant, about 1 minute.
Increase the heat to medium-high and add both cans of tomatoes, the stock and cream. Bring to a brisk simmer, reduce the heat to maintain a low simmer and cook until slightly thickened and the flavors have melded, about 20 minutes.
Puree the soup with an immersion blender until almost smooth. Add the nutmeg and season with salt and pepper. Serve in cups or small bowls and garnish with the chives.