Whales are no more or less an important part of the food chain than most other animals.
This century the whaling industry removed at least two million large whales from the Antarctic food chain, and the result has been a substantial disturbance in the ecosystem. It's rather like removing a lot of bricks from a house and hoping the whole thing won't fall down. Humans are playing the same game with many other aspects of the eocsystem globally, from rain forests to the atmosphere. Species by species, it's a subjective call. No it wouldn't.