Preheat oven to 400 degrees F (205 degrees C).
Cook rice according to package instructions. Use a fork to fluff up the rice once it is done.
Heat a sauté pan or skillet over medium-high heat. Add chorizo and diced onions. The fat released from the sausage is enough to cook the onions. Add red peppers and a pinch of salt, and sauté for another minute. Turn off heat. Add 3/4 of the chopped apples, thyme and orange juice and stir. If you're using a skillet or a heat-proof sauté pan, transfer it directly into the oven. Otherwise, pour the sausage and apple mix into a baking dish, and transfer to oven. Bake for 15 minutes.
In a large bowl, mix rice and the baked sausage and apples. Add remaining apple chunks, more salt and pepper, chopped chives, and a bit of lemon juice, if you like. Serve immediately.