A big problem with that is where to find whale-sized equivalents of uteruses to gestate the clones.
I think Kirk probably never really intended to "repopulate the species". He needed the whales only tell the probe to go f
23rd century genetics has to be way more advanced than 21st century so Timo is right. Once they got a hold of G & G's DNA they probably could have easily cloned a whole herd of them in a lab if they wanted to.
Now, whether or not they would choose to do that is certainly up for debate. I agree that in the post-Khan world they would certainly be hesitant about playing God with genes but at the same time, they might assume if the 2 humpbacks died out again that the Probe would come right back and they'd be back in the same situation.