What is the thesis of The Boys from Brazil?
I would argue that the thesis is "Scientific progress has no absolute morality in itself; it is only a tool to be guided by the morality of those who use it." While the protagonist and antagonist are clear, and primarily represent good and evil, the boys themselves are not judged one way or another. They simply are-they could not choose to be cloned, & they cannot choose the conditions of their lives. Thus, Liebermann lets them live. Some may say he is risking another Hitler, but he is subscribing to the idea of a child's environment being more important than his/her DNA.
Although such cloning currently is impossible, cloning of cells and certain animals has been achieved. In the years after Levin wrote this book, much was done to produce changes in fetuses and to develop certain characteristics within them. Indeed, many aspects of a child can now be determined with enough money. Would you like blue eyes & blonde hair? No problem! We will soon have designer children in the same way we now have designer dogs. It is conceivable that the sort of cloning represented in this novel will become scientific fact. Levin takes no moral stand on the ethics of such a scientific feat. He allows the reader to decide, based on who is manipulating the borrowed genetic material.