Because the Guardian was their ticket home and the Guardian decided when they left. I imagine if things had been different Kirk would have done some heroic insanity to make it LOOK like she got hit by the car and then whisked her off to the future.
History probably records her going after 'her' whales and never being seen again and her death being blamed on poachers.
Especially given the oddball nature of Spock. You'd see some creepy forensics sketch artist recreation of Spock in robes in her missing persons segment with the account distorted to make it sound like he's the leader of a new age cult.
Has she appeared in any later trek fiction? Given Cetation Ops is a thing by the time of TNG she probably was at least a consultant for the Federation when it came to humpbacks.
Also depressingly. All they did was delay the extinction of humpback whales by a few decades or so. Their kid, or another down the line, may well be around by the time of TNG, but with no other breeding pairs, they're the last as the Federation seems very... cloning adverse..