Preheat the oven to 350°F (175°C). Line a baking dish or rimmed baking sheet with parchment paper.
Juice 1 blood orange into a large mixing bowl.
Add the balsamic vinegar, soy sauce, molasses, honey, minced garlic, halved onions, ground ginger, paprika, kosher salt, and melted coconut oil to the orange juice; whisk until combined.
Add the chicken thighs to the bowl and rub the glaze all over each piece so they are evenly coated.
Place the coated chicken in the prepared baking dish and pour any remaining glaze over the top.
Slice the remaining blood orange and arrange the slices in the dish with the chicken; scatter the radishes and thyme sprigs around the chicken.
Bake for 20 minutes, turning the chicken once halfway through the cooking time to promote even browning.
Remove from the oven, season with ground black pepper to taste, and serve.