Preheat oven to 400 degrees F. Lightly spray a 1.5-quart baking dish with olive oil cooking spray.
If you need to cook the spaghetti squash: Pierce the spaghetti squash in a few spots with a sharp knife. Microwave 6 minutes; turn to the other side and microwave 6 more minutes, until soft to the touch. Let stand for 5 minutes to finish cooking. Using a sharp knife, cut the spaghetti squash in half lengthwise. Allow to cool 5 minutes, until easier to handle. Scoop out the pulp and seeds from the center, then rake a fork back and forth to remove strands of the flesh onto a bowl. Set aside.
In a large bowl, lightly whisk the egg. Add the sour cream, kosher salt, black pepper, dried thyme and minced garlic. Whisk until smooth.
Mix in the cooked spaghetti squash and the shredded cheese.
Transfer the mixture to the prepared baking dish. Bake until browned, about 40 minutes (it will smell wonderful!).
Allow to cool 10 minutes, then scoop into plates, or if you're patient, carefully cut into squares and serve.