Difficult. We have a troubling capacity for meta-behavior, where we notice how we're thinking and try to change it.
More likely, breed for non-violence and contentment. These are endocrine (?) systems that are immediately available to genetic engineers for tinkering.
Of course, you are still left with the problem of how to "retire" obsolescent models. Perhaps the new models could be engineered with the ability to eat foods that are toxic to the old models. In this way, simply turning over increasing quantities of agricultural land to production of the new foods would quickly push "old" food prices beyond the reach of (most of) the old-model human. Without need for overt action, the whole "retirement" process could proceed in an entirely covert and deniable manner.
Even if you could not explicitly breed for loyalty and obedience, simply reducing the variance in the expressed phenotype would make managing and controlling the general population much more straightforward. If everybody responded to stress and fear in a similar way, it would make it much easier to use these tools as instruments of control.
More likely, breed for non-violence and contentment. These are endocrine (?) systems that are immediately available to genetic engineers for tinkering.