Yes, astronauts in orbit for long periods can be prophylactically treated with medications for osteoporosis and muscle-stimulating medicines to prevent atrophy. In fact, this is already being done. Astronauts often take a combination of medications, including bisphosphonates, to prevent bone loss due to low gravity and muscle-stimulating medications to prevent muscle loss. Exercise is also an important part of preventing bone and muscle loss in astronauts, and many astronauts take part in regular exercise during their missions.