"The fault is not within the stars, it is within ourselves!" What we do with this technology will be determined by what individuals decide what is "moral" for themselves. Maybe some will see it as an abomination of nature to have a cloned organ. So be it. They won't have to buy one. Business will certainly drive the process, since it will supply what is in demand, but whatever "morally grey" areas that are created will only be so when people decide how to use the technology, and others disapprove of that method of useage. Certainly, creating an army of grunts through malgenics would threaten individual rights, and the appropriate government response is to forbid that, since government, when working, is supposed to defend rights.
Eugenics, on the other hand, has less of an argument--who wouldn't want to see the race improved? (but now we're into "The Wrath of Khan...." and guaranteed there will be pitfalls along the way, but that's no reason to not do it.)
Hopefully, cloning will continue to develop without moral objections, and the useage and development of such technology will remain and individual choice, as moral choices can only be, as only individuals can assign a value.