Cook the gnocchi. In a separate pot, melt the butter, add the flour and salt, combine with a whisk. Slowly add the milk; stir continuously until thickened. Stir in oregano, basil and pepper.
Stir in half the Fontal and half Parmesan cheese, then gently fold in the Gnocchi.
Transfer it to the baking dish and sprinkle with the remaining Fontal cheese and Parmesan cheese. Top with fresh thyme if desired, then bake until cooked.