Combine the orange juice, lime juice, smashed garlic, jalapeno, 1/2 teaspoon salt and a few grinds of pepper in a blender. Puree until combined, then let sit 5 minutes. Turn the blender back on and slowly pour in 1/2 cup olive oil. Remove 1/4 cup of the mixture and set aside for the marinade. Add the mint and parsley to the remaining mixture in the blender and puree again until smooth; season with salt and pepper. Transfer the sauce to a bowl; cover and refrigerate.
Season the chicken thighs generously with salt and pepper. Place in a large bowl and add the reserved 1/4 cup marinade, the minced garlic, cumin and oregano. Rub all over the chicken until evenly coated. Cover and refrigerate 1 to 4 hours.
Preheat the oven to 450˚ F. Let the chicken come to room temperature while the oven preheats. Toss the plantains and red onion on a rimmed baking sheet with the remaining 2 tablespoons olive oil; season with salt and pepper. Spread out on the baking sheet. Nestle the chicken, skin-side up, and orange slices among the plantains and onion.
Roast until the plantains are tender when pierced with a knife, about 20 minutes. Remove the plantains to a cutting board and stand them up on a cut side. Flatten the plantains with the bottom of a measuring cup or ramekin, then return to the baking sheet, setting them flat in the pan juices.
Return the pan to the oven and roast until the chicken is browned, crisp and cooked through, 20 to 25 more minutes. Sprinkle with chopped mint and parsley; serve with the sauce.