Yes, natural whale deaths are part of the deep ocean ecosystems. With a natural death, organisms in almost all parts of the food chain benefit and ultimately nothing is wasted. A diverse assortment of bacteria from decomposition and consumption of the whale corpse provides nutrients to worms, fish, jellyfish etc. Also, during the process, carbon is recycled and dispersed throughout the ocean, and some may even get back to provide nutrution to living whales.
Yes, whales must die for our ecosystem to sustain itself, but the same is true for all life on the planet. The questions asked by some are first, is hunting of whales is necessary to maintain their sustainable population? Secondly, is it moral to hunt animals that are sentient and self aware, particularily to be used as food. They have historically been protected because of delicate populations, so I would say that no they do not need to be culled for population control. The morality of hunting intellegent animals is sort an "eye of the beholder" inssue.
We, as members of a society here on earth, are not God. No benefits to killing whales in the name sustainability have been disclosed to societies to determine any benefit to the ocean, deep or shallow. I would suggest to all reading this answer raise their hands in all efforts to legally killing any such creature of God.
Many researchers and other environmental scientists have long underestimated the important role whale play in protecting the survival of many of living organisms in the ocean. Research now shows that an increase in the number of of large whales leads to a healthier ocean. These whales spread nutrients when they feed that help many other creatures.