My take on this is that genetics and environment work together as it does in most cases (always a safe bet). However, as you have alluded to, having a conscience is definitely a product of higher brain function (ie, smaller, simpler animals appear to have less of a conscience if any ..while those capable of higher brain function - having a more complex frontal lobe - have a greater sense of it thus have a greater feeling of guilt associated with the wrong they might see and do. And I do agree that survival does preceed this ability, else no animal would kill another for fear of the guilt that would come along with that ..and we would die off and quickly become extinct. But I do think you can be conditioned otherwise (ie, many humans would die before killing and eating another human being, even if it were necessary for their survival).
Now, take my cat for example. Though feed very well at home, she will still go outside and look for rats, chase birds and stomp on grasshoppers etc, and just follow her instinct and kill without any regret .. and just leave it there dead. This is mainly becauase she has the inability to fully process pain, and death, and thus her conscience is probably very limited to what she did that has had a direct negative reprocussion to her in the past ..that is to say, if I had physically conditioned her not to do this. So, not having the intelligence to understand what is right and wrong herself, and cannot fully grasp that all animals feel pain and not just her ...there is little thought that goes into considering the morality of it, and thus little to no guilt from it. Though, she still has some ability.
Assuming the inclination towards higher brain function in the animal, I think environment is the other very large piece of the pie that probably relates more to the degree of integration and sense. It's been years since I've taken a psychology course, but I vaguely recall what was defined as the "superego" ..though, from what I do remember, it consisted of all those societal rules we had integrated throughout the years that we put above our own ego and id most times, depending.
Most people feel bad when they steal (if they steal), and even worse if they steal from the poor for instance (most probably wouldn't do it). It's there in most people despite the environment they grow up in, but I do feel environmental condition just brings out all that inherent potential.