Cut 2 onions crosswise into 1/2-inch thick slices. Coat a medium nonstick in a single layer; sprinkle with the salt, and season with pepper. Cook, without turning, until undersides are deep golden brown, about 3 minutes. Turn, and cook until soft, about 4 minutes more. Reserve in skillet with heat off.
Bring a small pot of water to a boil. Meanwhile, finely zest half of the grapefruit. Add zest to pot, and boil 3 minutes. Remove zest with a fine sieve, and set aside. Zest remaining half of grapefruit into long strips; cover strips with a damp paper towel, and set aside for garnish.
Cut pith from grapefruit; discard. Working over a bowl to catch any juices, cut segments from membranes, letting them fall into bowl. Squeeze the remaining juice from membranes into bowl.
Bring 1 1/2 cups water, the stock, and 1/4 cup grapefruit juice from bowl to a bare simmer in a medium saucepan over medium heat.
Meanwhile, finely chop remaining onion. Heat oil in a large (6-quart) heavy bottom pot over medium heat until hot but not smoking. Add chopped onion; cook, stirring occasionally, until soft and golden brown, 4 to 5 minutes. Add rice; stir until coated with oil, 1 to 2 minutes. Add wine; stir until completely absorbed.
Stirring constantly, add simmering stock, 1/2 cup at a time, letting rice absorb each addition before adding the next. Stir until all stock has been absorbed and rice is creamy but al dente, about 20 minutes. Stir in grapefruit segments and reserved zest (excluding garnish); cook 3 minutes more. Season with pepper. Stir in chopped thyme, butter, and cheese.
Meanwhile, reheat the reserved onions over medium-low heat. Divide risotto among four bowls. Garnish each serving with onions, the reserved zest, and a sprig of thyme.