Is there any reason (other than belief systems formed from social conditioning) why death has such a foothold in humanity?

The first reason is guilt. The body, soul, and spirit struggle for supremacy and control in our lives. While alive, the body is in control. Ignorance tries to tell us that the body is an unholy and unworthy vehicle for our existence. Thus, we try to prove that we are worthy of life.

What about the higher stages of evolution during physical life? Which part of us is in control then?

It becomes a collaboration of integrated diversity. In a resurrected being, the body, soul, and spirit combine to form a vehicle of expression consisting of spiritualized, or incorruptible, matter.

Are there other reasons why death persists?

Most are not fully committed to life, and we have a sentimental view of death as a place of blissful repose, constructed to comfort those who lose loved ones.