That'd depend on what the whales said to the Probe. If it became obvious that the whales were transplants, and the Probe was happy with it
, then the Probe might not really care about whether there were whales there on its putative next circuit. Extinction would be all right, as long as somebody explained it to the Probe. If the Probe just chatted with two very confused whales who had no idea of what was going on (the likeliest scenario) and perhaps were incapable of reasonable dialogue anyway (a possible scenario, even if Spock's intuition on the subject would then be proven wrong), it could easily figure out on its own that the two were transplants. And if the Probe realized that whales were gone save for these two, and wasn't happy with that state of affairs, it might have left a message to the parties responsible to do something about it.
If there was
actual communication going on there, rather than just the Probe verifying that mindless beasts were making the expected mindless noises, Universal Translator analysis should tell Federation science what was being said, and the above possibilities could be verified or discounted.
Also, as far as "circuits" go, there should be about 300 years to figure out what to do about the next visit, as obviously the Probe hadn't been anywhere near Earth between the late 23rd century and the late 20th or it would have been observed. We can probably extend the circuit length beyond that by remembering that Vulcans and other aliens had been around and watching long before Earth got its first proper radars...
But then, your shrimp argument is invalid.
I'm curious - what about it is invalid? (Not that it was ever meant to be taken particularly seriously.)
If humpbacks stop contributing to the carnage of krill, the oceans will adapt to this new state of affairs and find a new equilibrium or steady state. If the humpbacks are reintroduced, the shrimp population will face a second ecological imbalance and thus "the oceans will be unhappy" about it. Reintroduction thus poses risks that might not be worth taking.