I don't think that many people hated them or regarded them as ugly, per say (With exception to the Halo 1 jackals. oh god). But noting the evolution of species, it is believable that at an early stage, they might have splintered off into a separate species due to climate, but thanks to their culture, or thanks to the Covenant, they came together as a single species. One has to remember, the birds we see today are still very close to the dinosaurs that once roamed the Earth.
That, and 343 couldn't use Bungie's design as their own, and so needed to modify them. What better way than to change them drastically? Think of these reptilian jackals as a off-shoot of the species. There was, in one of the early games, an amphibious jackal concept. (What a dreadful idea)