Preheat oven to 350°F Coat a large skillet with cooking spray. Heat skillet over medium heat. Place turkey, onion and chili powder in skillet and cook until turkey is browned, stirring occasionally to break up meat, about 8 minutes. Remove turkey mixture from skillet and set aside.
Place skillet over medium-high heat and add flour. Gradually add milk, stirring with a whisk until blended. Bring to a boil and then reduce heat to medium; simmer until thickened, about 2 minutes.
Remove skillet from heat; stir in turkey mixture, jalapenos and cumin.
Wrap tortillas in damp paper towels and microwave on HIGH until softened, about 15 seconds. Place 1 tortilla in bottom of a 9-inch pie plate. Spread 1/3 of turkey mixture over tortilla. Spoon 1 cup of tomato on top and sprinkle with 4 tablespoons (1/4 cup) of cheese. Repeat layers with remaining ingredients ending up with 2 tablespoons of cheese.
Cover pie plate with aluminum foil and cook until cheese melts and filling is warmed through, about 15 minutes. Let stand, covered, 2 minutes before cutting into 6 wedges.