Firstly, your history is a little bit selective: the only people who tended to directly benefit from whale products in the past were the rich aristocratic classes who could afford to purchase them. Whalebone corsets and whale-derived cosmetics were the property only of the wealthiest ladies of the era. Likewise, very few houses could afford to be entirely lit by whale-oil lamps. For the working classes, who made up the majority of the population, such items were unaffordable luxuries.
Secondly, while we can look back pragmatically and say that whaling had its place in the industrialisation of western society, the sad fact is that the more and more we learn about whales, the more our rapid decimations of their population seems like a crime against nature. These are highly intelligent animals, possibly second only to humans in terms of cognitive ability. Not only have they developed advanced forms of sonar communication that allow them to communicate with each other over vast distances, certain species have developed complex songs that are repeated and slowly changed over time. Moreover, science is proving with ever greater certainty that certain whale species exhibit self-awareness, and may be capable of higher forms of cognition than we had ever though possible.
No matter how you feel about PETA, or whether whaling helped industrialise the West, whaling was wrong, just as slavery and apartheid were wrong. Wales never posed a threat to us. We had no need to venture into their territory and start killing them off in such huge numbers. That we did is one of the great shames of humanity as a species.
I would hope that Ubisoft will shine a light on the horrible ethics of whaling, but I doubt it. An annual series is not exactly the sort of place developers go to in order to write commentary on the nature of whaling, and if Ubisoft turn it into anything more than an 'action-packed thrill ride', I'll be surprised.