Preheat the oven to 375° F and grease a 9-by-13-inch baking dish with butter. In a large nonstick skillet, heat the olive oil over medium heat. Add the onions and cook, stirring often, until softened and lightly caramelized, 20 minutes. Transfer to a large bowl.
To the skillet, add the butter and cook, stirring often, until browned and nutty in aroma, 5 to 6 minutes. Transfer to a blender and let cool.
To the blender, add the cottage cheese, sour cream, salt, eggs and black pepper. Blend until smooth, then add to the large bowl with the onions.
Bring a large pot of salted water to a boil. Add the egg noodles and cook until al dente, 7 minutes. Drain, then add to the bowl along with the sage and thyme. Toss until well coated.
Add the noodle mixture to the prepared baking dish and smooth the top with a spatula. Bake until golden brown and set, 45 minutes. Let rest for 5 minutes, then slice and serve.