My wife and I were just reading an article on IGN dicussing PETA's reaction to whaling in Assassin's Creed. They reported that a spokesperson from Ubisoft stated:
"History is our playground in Assassins Creed. Assassins Creed IV Black Flag is a work of fiction that depicts the real events during the Golden Era of Pirates. We do not condone illegal whaling, just as we dont condone a pirate lifestyle of poor hygiene, plundering, hijacking ships, and over the legal limit drunken debauchery."