Combine beans and ground cumin in a small bowl.
Place 1/4 cup bean mixture on each of 4 tortillas; mash with a fork to within 1/2-inch of the sides. Sprinkle each portion with 1 teaspoon jalapeños; top with 2 tablespoons chiles and 1 tablespoon black beans. Arrange 2 tomato slices on each portion; top with 3 tablespoons cheese, 1 teaspoon cilantro, and remaining tortillas.
Spoon yogurt onto several layers of heavy-duty paper towels; spread to 1/2-inch thickness. Cover with additional paper towels; let stand 5 minutes. Scrape into a bowl using a rubber spatula; cover and refrigerate.
Place a large nonstick skillet coated with cooking spray over medium-high heat until hot. Add 1 quesadilla; cook 3 minutes on each side or until golden. Remove quesadilla from skillet. Set aside; keep warm. Repeat procedure with remaining quesadillas. Cut each quesadilla into 4 wedges. Serve warm with yogurt cheese.