1. Bring 6 quarts water to a boil in a large pot; season with salt.
2. Meanwhile, in a 10- to 12-inch skillet, heat olive oil over medium heat until almost smoking. Add onion and red pepper flakes; saute until translucent, 8 to 10 minutes. Add jalapenos; saute for 1 minute. Add zest and juice; bring to a boil, and boil for 1 minute. Remove from heat; stir in butter, and season with salt and pepper. Set aside.
3. Drop pasta into boiling water and cook until tender, 1 to 2 minutes. Drain.
4. Toss hot pasta into pan with lemon mixture; return to medium heat. Stir together gently. Add pecorino; toss quickly. Transfer to a warmed serving platter. Serve immediately.