In a 5- to 6-quart pan over high heat, bring about 4 quarts water to a boil.
Add penne and cook, stirring occasionally, until tender to bite, 10 to 12 minutes.
Drain.
Meanwhile, in a 10- to 12-inch frying pan (with sides at least 2 in. tall) over medium heat, stir onion and garlic in olive oil until limp, 3 to 5 minutes.
Add lemon peel, lemon juice, butter, and scallops to pan with onions. Bring to a simmer and cook until scallops are opaque but still moist-looking in the center (cut to test), about 6 minutes.
Add pasta and basil to scallop mixture and stir until heated through.