sticky traps around the plants to catch these flies. However, with more research there doesn't seem to be any remedy for this problem. The sticky traps may have some effect but certainly not a cure-all. We went ahead and placed several through-out our pepper plants and as been somewhat useful in capturing some of these pests. We did cut off some leaves but will do so sparingly in the future as to not hurt the plant.
Above are Serrano Pepper plants that seem to be thriving. In the back you can see a sticky trap that seem to be doing the job.