If a beat-up old Klingon bird-of-prey, modified using 1986-era materials, was able to collect two adult humpbacks and bring them back to the 23rd century, if there is concern about the whales' long-term prospects, why not just send a couple of Excelsior-class ships back to about 1600 using the slingshot maneuver and collect some more whales until enough were present to successfully re-establish them for the long term? Not exactly standard Starfleet procedure, granted, but if it means risking a return visit from the Probe it might be worth it.
I did a little checking and prior to the beginning of commercial hunting in the 18th century, whale populations reached around 125,000 or so, although there's no way to know for sure. It seems to me that with proper communication, Starfleet could round up enough aquatic volunteers to bring Back To The Future
without disturbing the whale population too much overall, and going that far back in time means that the risk of detection by the human population of the time would be negligible.