I don't see a problem with it. It's not like it's just a bunch of men with clubs killing animals for the heck of it.
They use the body for whatever they need. It provides a living for people.
The sort of people who complain when we are hunting animals that aren't endangered for actual reasons that benefit people and their countries are idiots.
You might as well complain that we're killing too many chickens or cows.
The moment these animals become endangered, they'll be protected and hunting them will stop until their population regrows. Of course you'll get the odd poachers, but the population will regrow. We're not killing them to destroy their species. That wouldn't benefit us at all if they died off. We can't use their body if they no longer exist.
And the reason why the job is done with a club, rather than say, a gun, is because guns use ammunition which costs money. It's simpler and cheaper to kill an animal that can't defend itself or escape you with a melee object.
Also, who cares if it's horrible that they're being killed with a bat or a club. You'd still complain if they were killed with a gun or a knife. As far as the seal is concerned, it's going to die. I don't think an unintelligent animal is really going to care if it's shot in the head or clubbed in the head.