The Federation should be making long term plans to ensure the survival of the species. That would include selecting planets where they could be settled. That's something that should be undertaken ASAP so that they can be transplanted as soon as they are ready.
How are the whales in danger in Earth's oceans? No one hunts whales in a world where replicators (or at least "food slots") supply everything humans need.
As northern humpbacks, George & Gracie are tied to Earth's northern hemisphere. Northern hemisphere humpbacks don't travel to the southern hemisphere. Would they cope being transplanted to an alien world's oceans?
Are you also going to infest an alien world with krill, too, or will the transplanted humpbacks be expected to eat local food?
Has Earth transplanted examples of every other lifeform to other planets too? Have we not learned the dangers of animals going feral in places they didn't evolve in? Has every UFP world also transplanted their animals and plants? It's gonna be a messy galaxy.
Humans are being settled on all sorts of planets. Sherman's planet was being seeded with Earth grain. People can eat the fruits of alien worlds, Kafarian Apples for instance. Why should humans have all the fun and the whales HAVE to stay home?
As far as them being safe on Earth, yes Earth is safe. Except for:
The Xindii sphere
Romulan plasma torpedos
The Doomsday machine
Nomad
V'ger
Any hostile alien race that happens to develop a Genesis torpedo.
The Breen/Dominion alliance
The Klingons
Stellar core fragments
Nearby black holes like the one Voyager 6 fell into
Space amoebas
Protomatter being thrown into the sun like the Bashir changeling attempted at Bajor.
Supernovas like the one that destroyed Romulus
And let's not forget, red matter black holes like the one that ate Vulcan and could have done the same to Earth except for Kirk.
Other than that, Earth is perfectly safe.
We almost got wiped out once because we didn't have the whales. It's a good idea to have a backup.
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