Heat oven to 425°F. Remove giblets and neck from chicken. Rinse chicken inside and out with cold running water; drain well. Pat dry with paper towels.
Grate 1/2 teaspoon rind from orange and set aside. Cut orange into quarters. Sprinkle 1/2 teaspoon salt inside cavity of bird. Stuff chicken with onion, orange quarters, bay leaf, and thyme. Place on rack in large foil-lined roasting pan. Sprinkle with remaining salt and pepper.
Roast chicken 1 hour and 15 minutes. In small bowl, combine reserved orange rind with glaze ingredients, and brush over entire chicken. Roast 15 minutes more, or until meat thermometer inserted in thickest part of chicken thigh reaches 175°F and juices run clear. Let the chicken rest for 15 minutes before slicing.