Remove all fat from the chicken breast halves and pound them slightly. In a mixing bowl combine the lime zest and juice and season with 1/2 teaspoon salt and 1/4 teaspoon dried red pepper flakes. Coat the chicken with this mixture, and transfer it to a zippered plastic bags. Press out all the air and refrigerate until ready to grill.
Make the salsa. Over a mixing bowl, grate 1 teaspoon of the orange zest. Peel away the skin and white pith from the oranges. Over the bowl with the zest, cut between the membranes of the oranges to release their sections, and combine them with the zest. Squeeze remaining juice from the membranes over the orange sections and stir in the pepper, chives, olive oil, and lime juice. Season with salt to taste and a pinch of dried red pepper flakes, if you wish.
When ready to eat, lightly oil a grill or broiler pan. Remove the chicken and arrange on the rack and grill or broil for about 3 to 4 minutes a side. Remove to a plate (grill the eggplant next) and serve at room temperature with the salsa.