Heat 2 tablespoons of the oil in a medium saucepan over high heat, add the onion and cook until soft, 3 to 4 minutes. Add the juice and thyme, bring to a boil and cook, stirring occasionally, until thickened and reduced to approximately 1/2 cup, 20 to 25 minutes.
Strain the mixture into a bowl and whisk in the syrup, soy sauce and black pepper and let cool to room temperature. Can be made 2 days in advance and brought to room temperature before using.
Brush chicken on both sides with the remaining oil and season with salt and pepper. Grill until golden brown on both sides and just cooked through. Begin brushing with the glaze during the last 5 minutes of grilling. Remove to a platter and sprinkle with the green onion. Garnish with grilled citrus.