In a small saucepan combine the water and quinoa. Bring to boiling; reduce heat to medium-low. Cook, covered, for 10 to 15 minutes or until water is absorbed. Remove from heat. Stir in salsa.
Meanwhile, in a small bowl use a fork to beat together whole eggs and egg whites. Beat in milk and salt. Coat a medium nonstick skillet with cooking spray; heat skillet over medium heat. Pour egg mixture into hot skillet. As eggs begin to set, fold mixture over on itself, continuing to fold until fully cooked. Cut egg mixture into four portions in skillet; top each with 1 tablespoon of the cheese. Remove from heat.
Place a tortilla on each of four serving plates. Lay chile peppers flat to cover half of each tortilla. Spread chile peppers with quinoa mixture. Top with eggs. If desired, garnish with tomatoes and/or cilantro. Roll up tortillas. If desired, toast burritos in a large dry skillet over medium heat until light brown and crisp.