There are species of eagles (and other birds) whose young kill their siblings by slow, torturous pecking or a hefty push out of the aerie until there is only one left to feed.
To our human sense of overdeveloped morality it seems wrong, but that is the way the species has evolved. Why should someone mess with millions of years of development? Tinkering around with nature’s flow and interpreting the acts of animals through the lens of a human’s morality is what got many animals into trouble in the first place; tinkering around with the flow some more isn’t going to fix it.
If the way a species develops turns out not to be optimal, natural selection will weed them out; with or without human interference. The way their species has adapted to procreate and raise their young and gather food… it’s all done for a reason and that reason should not be tampered with.
Since the fact that it is a recorder of event’s responsibility to only record and not interfere has been covered, the only remaining element (as I see it) to the question is the question of “what harm could it have done to the natural order of things to have removed the cubs and put them in a zoo until they could later be released?”
There are several problems with that scenario. When a lioness’ cubs are killed, she immediately stops nursing and becomes able to conceive. Removing them, however, does not (someone correct me if I’m wrong on this point). By doing so, the conquerer and new leader of the pride cannot impregnate the lionesses, and optimal breeding time is lost. If conception is able to take place shortly thereafter, they may be pushing their window of opportunity to raise cubs successfully, and if they cannot that season, then an entire generation of cubs is lost.
Also, lion cubs raised in captivity have a lower than normal success rate once released back into the wild. A lion’s survival depends upon being a part of a pride. Some can and do survive for a time on their own, but many end up dead at the hands (claws) of a pride’s dominant male whose territory they inadvertantly invaded, or starve to death (there’s a reason they hunt as a pack, their prey are generally much faster than they… solitary lions eat more carrion than catch their own food). Releasing unindoctrined cubs into the wild is about as sure a way of getting them killed as anything because they must find unclaimed territory, defend said territory against older, stronger lions, and hunt on their own. Their only real chance is to either take over a pride by challenging and killing the dominant male (and then guess what happens to the cubs), or by being allowed to join a pride, which is more common of female lions than male.