I don't think taking medical leave will help. Avoiding headache triggers will be the most important. If cognitive load causes an increase in headaches, you should try to moderate your efforts.

As a pilot, you should be aware of any cognitive changes when flying at higher altitudes. Studies show that people who have suffered concussions are more sensitive to altitude that those who have not suffered a concussion. I had to stop flying because I was making mistakes when preparing to land after flying at 10,000 feet or so. The study showed notable cognitive performance declines at only 8,000 feet for those who had a concussion history.