Evolution of small things like algae and the krill which feed on it and feed the whale is quite fast. Single celled organisms reproduce on the scale of 20 minutes and hold immense amounts of genetic diversity in their populations to facilitate the success of a better adapted line almost immediately. Additionally, they are adept at horizontal gene transfer from other well-adapted organisms.
This would be great news if the whale literally only required krill to survive, but complex megafauna have complex needs, so the ability of krill and other small creatures to evolve is largely irrelevant in a discussion regarding the ability of megafauna to survive. This is especially true if you read TFA and see that the whales already adapt to eat different things as necessary.
My point is, for instance, that they need appropriate temperatures in the water. Again, nothing survives PURELY based on caloric intake. It does not matter much at all if krill evolve.
It could easily become this fast or even faster, if we would just stop worrying so much about "playing god" and focus instead on getting good at this job. We don't have much time for this either, as AI is on the trajectory to take over that mantle in the next decade or three, whether we like it or not.
But seriously, we may not have much choice. Natural evolution stopped being able to adapt to environmental changes after it created us; genetic engineering is essentially the only way to make biology adaptable enough again.
The next question is which traits to do you choose and the next question is which traits are better, because choices will imply ordering, and then you open a big can of worms that last time killed millions of people. So maybe there's other ways to avoid doom that didn't create doom last time we went down the path.
Unpopular opinion for obvious reasons, but probably the only realistic one apart from just witnessing one extinction after another. Pollution and climate change aint going anywhere until we elevate whole world to the level of say western Europe.
But since we humans are pretty arrogant with our wisdom and lack long term patience, I can see many ways where well-intended meddling can end up in catastrophe overall.