The boss battles in Assassin’s Creed 4: Black Flag aren’t always about fighting against a super strong opponent who has 18 life bars and some ridiculous one-hit kill attack. In fact, the final boss battle against Loreano Torres doesn’t feature any of that. What it does consist of is an elaborate maze of death light and mayhem culminating in an aerial assassination of Torres. Killing Torres isn’t even the real objective here, it’s essentially the reward you get for navigating all of the dangers leading up to the kill.
As you approach the observatory, you don’t have much to worry about. When you see the soldier get taken down by the light, you could run immediately to avoid the next surge, but it’s best to stay back and wait, then run forward after the next rotation.