Perhaps you think that Prometheus will remain loyal to the Omegas rather than to its goal, given that it knows that the Omegas had programmed its goal. But that’s not a valid conclusion: our DNA gave us the goal of having sex because it “wants” to be reproduced, but now that we humans have understood the situation, many of us choose to use birth control, thus staying loyal to the goal itself rather than to its creator or the principle that motivated the goal.