The great mark of a Star Trek episode was a thinly-veiled moral, some sign of deep thought as a commentary on the current social scene. The episode Let That Be Your Last Battlefield (the halfblack, half-white faced dudes) was all about a relavent cultural issue. Star Trek VI (which DiF has already covered) is about the fall of Soviet Russia and racism.
Star Trek IV is about... not pushing humpback whales to extinction, or else an alien probe will punish us?
Environmental conservation? Appreciating that we're not the only living things on the planet? Realizing that the damage we're doing to the planet could have long-term unforeseeable consequences?
Environmental conservation was an extremely significant aspect of the contemporary social scene, and one of its big slogans was, in fact, "Save the Whales." To make that the plot of the movie was doing exactly what Star Trek -- and science fiction in general -- does best.
Is it a little silly and on the nose? Sure. But if you're going to condemn it on those charges, while using as a counterexample the episode that made a racial allegory by literally painting actors' faces black-and-white, I'm going to be forced to call shenanigans.