I appreciate the reference. I understand the general idea behind the study and it's good that such science is done. The authors are also careful to note that there are so many uncertain parameters in their estimations and as such, their pre-harvest numbers have significant range. Moreover in their articles, they don't argue that whales shouldn't be hunted just because they have not reached pre-harvest population. They merely suggest that hunting quotas for whales species that have shown appreciable recovery like minkes could be reduced (but not eliminated) based on their estimations.
If we have to give up hunting animals until they reach pre-harvest levels, we will be forced to give up catching tunas, crabs, lobsters, sea-urchins... and the list goes on. And, as you mentioned, the marine environment changes over the 100 yr time scale (be it human-caused or not) so the local whale population may never reach the level 100 years ago, let alone even more distant past that the genetic study suggests. The current environment at a certain region may not be able to sustain the same number of whales that may have lived there 1000 (or even 100) years ago. What is important is that we monitor the change in whale population closely while we hunt small number of whales that won't profoundly affect the recovery process.
I mentioned it in this case to point out that whale poaching is much more difficult to pull off compared to other wild animals like kangaroos. Australians don't track the DNA data of 3 million+ kangaroos killed each year and consumed in the market whereas all whales distributed in Japan are accounted for. It is easy to imagine lots of kangaroos are hunted illegally and sold on the market, and once it is on the market, very difficult to track them. As I mentioned elsewhere, I believe it is helpful to put whaling in perspective with other animals hunted or slaughtered for human consumption.