Preheat the oven to 350 degrees. Coat a 13 x 9 inch baking dish with nonstick cooking spray.
In a 10 inch sauté pan, heat the oil over medium heat, then add the onions and jalapenos and cook, stirring, until the onion softens, 4 to 5 minutes.
Turn the mixture into a large mixing bowl. Add the beans, 1 cup of the sour cream, the cumin, and ground chile and stir until well blended. Spread the bean mixture over the bottom of the prepared dish and cover evenly with both grated cheese. At this point, the casserole can be refrigerated, tightly covered with plastic wrap, for up to 24 hours. Allow it to come to room temperature before baking.
Bake the casserole until the cheese is bubbling, 30 to 40 minutes. Remove the casserole from the oven, garnish with the cilantro, and serve the remaining ½ cup sour cream on the side.