Toss cranberries with 2 teaspoons olive oil, sugar, and thyme in a bowl. Pour onto a baking sheet.
Arrange butternut squash into a single layer on a separate baking sheet. Coat evenly with 1/4 teaspoon salt and pepper.
Bake cranberries and squash in the preheated oven until cranberries are softened and lightly browned and squash is tender, 15 to 20 minutes.
Bring water to a boil in a saucepan; add 1 tablespoon olive oil and 1/2 teaspoon salt. Remove from heat and stir in couscous. Cover saucepan and let stand until water is absorbed completely, about 5 minutes. Fluff couscous with a fork; let cool for 10 minutes more.
Combine the cranberries, butternut squash, couscous, celery, lemon juice, lemon zest, and the remaining 2 teaspoons olive oil and 1/4 teaspoon salt in a bowl.