Heat the oven to 400°F. Combine quinoa and its water in a saucepan, bring to a simmer, cover and cook over low heat for 15 minutes; rest covered for 5 minutes.
While the quinoa cooks, brush pepper halves with 1 teaspoon oil and arrange cut-side up in a 9-by-13-inch baking dish. Bake empty for 15 minutes.
While the peppers bake, heat remaining oil in a skillet and brown beef and onion for 7 to 8 minutes until the meat reaches 160°F. Drain excess fat.
Stir in beans, corn, salsa, chili powder, cumin and salt and simmer for 4 minutes until thick. Fold in cooked quinoa and divide among the softened peppers.
Scatter Pepper Jack over the filling and bake for 18 to 22 minutes until the peppers are tender and the centers reach 165°F. Rest for 5 minutes and serve two halves per person.