In a large soup pot, heat the olive oil over medium-high heat. Add the onion and cook, stirring occasionally, until soft, about 7 minutes. Add the chicken thighs, cumin, paprika, turmeric, cinnamon stick, 1/2 tsp. salt, and 1/2 tsp. pepper. Cook, stirring, for about 2 minutes. Add the stock, harissa, tomato paste, and tomatoes. Cover and simmer gently until the chicken is cooked and falls easily from the bone, about 45 minutes.
Take out the cinnamon stick and discard it. Remove the chicken from the broth and let cool. Skim any fat from the surface of the broth. Pull all the chicken meat from the bones; discard the bones. Tear the meat into 1-inch pieces and stir the chicken back into the soup.
Over medium-high heat, bring the soup to a gentle boil. Stir the soup constantly as you slowly add the couscous. Reduce the heat to low, add the mint and cilantro, and simmer, uncovered, until the couscous is tender, about 5 minutes. Stir in the lemon juice. Taste and add salt and pepper if needed.