Please make sure your therapist knows you're having headaches. There may be a simple reason for this such as head and neck position during the lumbar traction. Headache as a side effect of traction is common in a small number of people.
Most of the time the effect is not serious or long-lasting. You shouldn't really have to have pain or discomfort in another area of your body to help the problem area heal. Your therapist should review your case carefully. He or she will also help you weigh the pros and cons of traction versus other treatment.