Whaling—that is, shooting whales with harpoons and leaving them to struggle for an hour or more before they die or are hacked apart while they are still alive—may seem like something out of the history books, but this bloody industry still goes on today in the face of international condemnation, and it’s disgraceful for any game to glorify it. PETA encourages video game companies to create games that celebrate animals—not games that promote hurting and killing them. - PETA

I'm not sure that Ubisoft is trying to promote whale-killing in Assassin's Creed IV. It's just part of the history that goes in when making a game that is semi-realistic. With that said, I doubt too many people will play ACIV and then become so interested in whaling that they take it up in real life.