There are no absolute contraindications to needed and appropriate medications for a person with systemic lupus. Your doctor should watch for allergic reactions to medications, and watch for any connection between flares and estrogen or oral contraceptives.
People with lupus should be especially careful if they are prescribed sulfa antibiotics. These medications (Bactrim, Gantrisin, Septra) are often prescribed for urinary tract infections and may cause an increase in sun sensitivity and occasionally lower blood counts resulting in disease flares. There are also sulfa diuretics (water pills) such as Dyazide and diabetic drugs containing sulfa such as Aldactone.