First, you are naive to assume that belief in a soul is merely "religious". Countless philosophers throughout history have believed in a soul for non-religious reasons and some philosophers still believe in the existence of the soul for non-religious reasons (admittedly, materialism is the dominant view today). For instance, cf. Stewart Goetz and Charles Taliaferro's book A Brief History of the Soul.
Second, even if we don't have souls the question still makes perfect sense in light of personhood debates. Just imagine that by "soul" the people in the book/movie mean "that which makes us valuable persons with a right to life" instead of imagining "an immaterial substance that exists apart from the body."
Third, materialistic humanism has no ultimate grounds for morality anyway... So yeah the clones don't have souls and neither do non-clones in your materialistic humanist worldview. But the materialistic humanist also can't provide any objective reason for why we shouldn't cage some set of humans and harvest their organs. So it's not that the movie that collapses like a house of cards hit by a bowling ball... it's the so-called morality of materialistic humanism that collapses like a house of cards hit by a bowling ball.
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