(It's been a year or two since I've read LOTF, so memories may be a little fuzzy)
The irony is that throughout the book, the boys are portrayed as rogue savages and go to war against each other. When the navy officer arrives, his position shows that he is a part of war, the representation of war.
The officer is supposed to be a hero, an adult at last, someone sensible, as shown when Ralph desperately tries to explain the horrors of what the boys have done. However, it is quite ironic that their hero to rescue them from their brutal war, is a person who partakes in war. His war be more modernized and he may wear a nice clean uniform, but he too is a savage, just like the schoolboys.
