Preheat the oven to 350° F. Line 12 muffin cups with cupcake liners. Whisk together the flour and next 7 ingredients (through salt) in a medium bowl. In a separate bowl, whisk together the butter, egg whites, and vanilla. Stir in the yogurt, mixing until no large lumps remain. Stir in the molasses and maple syrup. Alternate between adding the flour mixture and protein to the yogurt mixture, beginning and ending with the flour mixture, and stirring just until incorporated.
Bake for 19-22 minutes or until the tops feel firm to the touch and a toothpick inserted into the center comes out clean. Cool the cupcakes in the pan for 5 minutes before transferring to a wire rack to cool completely.
To prepare the frosting, beat together the Greek yogurt, cream cheese, protein and stevia in a small bowl until smooth. Spread on top of the cooled cupcakes, and sprinkle with cinnamon if desired.