How would you even stick the Enterprise into this movie?
You can't land it in Golden Gate Park, eliminating the need for a common rendezvous point. Now how is Gillian Taylor supposed to find them? In a way that is cinematically interesting?
You could still build the whale tank abord Enterprise, but you couldn't crash the ship into the bay (not on the post-ST:TMP budget, anyway). You couldn't block a torpedo from the whaling ship with it. You'd be scanning for the whales from orbit during your next casual pass over the Pacific Ocean.
Might as well insert the fade-to-blacks every twelve minutes and have composer Leonard Rosenman add a ST fanfare every time the story cuts back to the ship.