I think one of the reasons we are able to suppress our instincts is because we see other people successfully doing what we desire to do. Can you imagine how much more nervous you would have been in the airplane on your first jump if you had never seen a skydive before, either from the ground or on video?
There is a big difference with your analogy of putting the gun to your head and flying a canopy. In our minds no matter how much talent and experience with firearms you have if you put a loaded gun to your head and fire it the outcome will be bad. With regards to canopies the outcome may not be bad, depending on your abilities. I don't see it so much as the suppression of a survival instinct but, rather, as the overestimation of our skills. A lack of knowledge also plays a part in this. Many of the aspiring swoopers out there, not all mind you, do not realize all of the dynamics involved and how to recognize them and what their effects can be. We are not afraid of what we don't know.