It's actually a pretty nifty allegory.
The damage as described in the episode would be even more obscure and slowly acting than global warming. Sure, it might be easier to measure, as we might assume "subspace weather" not to significantly confuse the observation of "subspace climate". But if it takes centuries or millennia of extreme overuse (such as in Hekaras) to create measurable effects, it's easy to argue that the best response would be to ignore the phenomenon completely. Odds are that warp drive will go away before any real damage is done - a bit like if oil and coal would run out two weeks from now, making their contribution to the greenhouse effect insignificant.
It's an interesting philosophical question and parallel: "What we do now is irrelevant. What our grandchildren do is irrelevant. But do we have the duty to ensure that our great-grandchildren do the right thing?"...