Most of us do seem to side with the most cuddly, the most mammalian, the most "charismatic" of the species harvested or hunted by man. Yet all life should have value, and the taking of any of it for food or other human needs should be viewed within that framework. Even those vegetarians who harvest seeds, nuts and fruits are terminating potential life (not sure how I feel about the ones that feed only on renewable parts like leaves)
I'm a biologist, too and am well aware of the affinity of people to want to save 'charismatic' species. If we all converted to being strict fruitarians, then perhaps no living entities would be killed to sustain us...except possibly the microbes we inhale. Ain't gonna happen, tho.
There are extensive, multi-billion industries already established for the harvesting of terrestrial and oceanic protein sources. Whaling will not affect whether people go to bed hungry or not. So, like you said, torpedoes away...