Whether or not you want to classify 'blinking an eye' as an instinct, it IS a trait that has 'survived' through the history of life forms. I think that both 'reactions' and instinct find their roots in history, and that certain automatic responses (whether they are sneezing or pursuing sexual relations) they have proven their worth, by not going extinct. No one consciously judges whether or not a trait is important, they sort themselves out. The animals that survive pass on their genes, and those that die don't pass them on (simple eh?). Those that are passed on MUST have survived because they are responsible for traits/characteristics that have aided in the animals survival.
Our moral behaviour has also aided our species' survival by being responsible for the way we have made a sciety: By now we can't even live in the wild anymore, because we are so adapted to the society we have created for ourselves. We are probably the only (omnivorous) meat eater that can't live on raw meat! This alone supports that we have changed over time. Why would god create people with internal organs and predatorial teeth/position of the eyes characteristic to meat eaters and NOT give us the possiblity to eat raw meat?!
Conclusion: Those traits that benefit our behaviour are more present in us than traits that don't support our survival. Our sense of morality might be related to personal conditions for one part (the laws we obey, the religious morals we choose to follow) but it also has deeper roots, because all people in the world share certain preferences for moral conduct. I don't think this is because god created them all, but because our common ancestors passed the genes that stimulated these traits to us.