Indoctrination is a key element of this novel, as the clones are brought up to learn very quickly about their "special" status and the ways in which they must not engage in activities that will damage their bodies so that their organs might not be able to be harvested. You might want to think about the advice that their headmistress gives them about not smoking when the central characters are at Hailsham as an example for this.
What strikes me above all in this excellent work of literature is the way in which none of the three central characters seem to feel that they are able to resist their fates. They have clearly been indoctrinated to such an extent that they see their separation through death as being inevitable and not worth fighting against. Consider the following quote as an example of this:
I keep thinking about this river somewhere, with the water moving really fast. And these two people in the water, trying to hold onto each other, holding on as hard as they can, but in the end it's just too much. The current's too strong. They've got to let go, drift apart. That's how it is with us. It's a shame, Kath, because we've loved each other all our lives. But in the end, we can't stay together forever.
Note the way in which separation is something that is seen as an unequivocal conclusion to this relationship. There is no option of trying to fight against the forces that seem determined to separate them, and Kathy and Tommy seem to meekly accept their eventual fates and deaths. They are clearly products of a system that have successfully brought them up to accept their fates without question or even the ability to consider that there might be otehr possibilities.