Along the same timeslines, alot of the beef meat we eat are from the males (sorry guys). You only need a few stud bulls to fertilise the breeding females, dairy cows (maybe you could investigate utilising the whalecows milk. I think you will have to invest in some scuba gear). Maybe your geneticallygenetic engineers can tinker with a couple of genes and make it obvious from a surface viewers point of view if they are about to harpoon a male or female. I'm thinking skin colour or something 'small' like that.
While you are thebusy genetically modifying the whales. If you track the whales you will figure out which ones are breeding faster and more often. Kill off the slow and lazy ones. Allow 'survival of the fittest' to take its course.
If you can keep tabs on the whales, co-ordinate all along the coastline and with your vast mobile armada of whale hunters (sorry, caring whale shepherds),you won't necessarily have to 'domesticate' and 'tame' the whales. Ostrich are farmed for both their feathers and meat and they are certainly not considered domesticated.
EDIT considering you new world only has plankton, krill and whales...No predators. You can remove the young from their mothers a few months (maybe 6months) after they are no longer dependant on mother's milk. No need to protect a youngster for 2-3 years if there is nothing to protect against.
You may have to move the young to some aquariums completely removed from the ocean so that they don't communicate with mother dear. Let mother grieve for awhile and a few months later to a year she could possibly be pregnant again. This will increase productivity!
The youngsters meanwhile are being handled and dependant of humans and will become 'friendly' and not perceive us as a threat (suckers). Once these youngsters are brainwashed they can be released back into the wild to feed themselves.
A few years later...yummy steak on your table.
I sometimes wonder about the way worldbuilding brings out the absolute evil in us all!