There is a HUGE difference between boiling crustaceans and boiling live eggs.
Crustaceans (shrimp, lobster, crawdads, etc) are all prepared by boiling them alive. This is done by bringing the water to a hard boil and then putting the crustacean in. It dies instantly and painlessly. They also have a much more simple nervous system than poultry, and are not believed to feel pain in the same way anyways.
Eggs on the other hand, are boiled differently. Typically the egg is placed in cold water, which is slowly brought up to boiling temperature. This would be a slow and excruciating death for the chick. And even if the water was brought to a boil before submerging the egg, it would still take several moments (if not more) for the temperature of the egg to get hot enough for the chick to die. So either way, that chick is going to be in a world of hurt before it finally slips away and out of it's misery.
I am all for using animals for human consumption, but humane dispatch is a must for me. And I just don't see how balut can be cooked without causing the chick significant pain.