The cases against hunting kangaroos and whales are totally different. Whales are endangered, but there are too many kangaroos. Hunting kangaroos would help control their population. On the other hand, we need to protect the whales that remain so they are not driven into extinction completely. Whales are also a popular food sources, but most people do not like to eat kangaroo meat.
There is a factual distinction between Japanese whaling and kangaroo culling in Australia. One is a nuisance, the other includes a variety of species which too often pushed to the brink of extinction. History is rife with historical accounts of whale populations being vastly in excess of what we know them to be today. Reducing the population of a public hazard like kangaroos does not legitimate an Ahab like quest to eliminate the leviathans of the sea.
Firstly, whales are not endangered. Some SPECIES of whales are endangered, but minkes, which are almost always the target, are absolutely not. Therefore, killing a whale is no worse than killing a kangaroo, as it does not harm the ecosystem. Being shot with a rifle is also no quicker than an exploding harpoon. In fact the kangaroo cull has a significantly crueler death rate than Norway, where 80% of whales are killed instantly. And meat is meat, and an animal always has to die for it. No meat is inherently more unethical than another, unless of course it is actually endangered or was harvested cruelly. What if a Japanese or Norwegian or Icelander walked up to an Australian and said "you shouldn't eat kangaroo meat because it is wrong to do so". What would you say to him?