Preheat oven to 450 degrees. On a rimmed baking sheet, arrange squash cut side down; cover sheet tightly with aluminum foil. Roast until tender when pierced with the tip of a paring knife, about 40 minutes.
Meanwhile, in a large saucepan, heat butter over medium. Add shallot, garlic, and sage; season with salt and pepper. Cook, stirring occasionally, until tender, 3 to 5 minutes. Add rice and 1 3/4 cups water; bring to a boil, cover, and reduce heat to low. Cook until tender, without stirring, about 25 minutes.
Remove rice from heat, and stir in cherries and pecans; season stuffing with salt and pepper. Season the inside of each squash half with salt and pepper. Dividing evenly, mound stuffing into halves, and serve.