Preheat the oven to 350°F (175°C).
Juice 1 of the blood oranges 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 bowl; whisk until smooth.
Add the chicken thighs to the bowl and rub the glaze all over each piece until evenly coated.
Line a baking dish or rimmed baking sheet with parchment paper and arrange the glazed chicken in a single layer.
Slice the remaining blood orange and tuck the slices among the chicken pieces. Scatter the radishes and thyme sprigs over the top, then pour any leftover glaze over everything.
Bake for 20 minutes, then turn the chicken once halfway through the baking time to promote even cooking.
Remove from the oven, season with ground black pepper to taste, and serve.