But now, the discussion question: What would people say if this experimentation were being done on puppies, or rabbits, or baby seals? Why are fruit flies different?
Because we as a society explicitly assign different levels of moral worth to different animals. Fruit flies have greater worth than bacteria or yeast but lesser worth than mammals, which in turn have lesser worth than primates or humans (as subcategories of mammals).
That's an inherent problem to in vivo studies: we're fine with experiments on bacteria or yeast but we'd all be horrified at unconsenting experiment on humans. There's a line, and we must draw it somewhere.