Holding hands can mean a number of things to different people, but it is not a ritual of prayer in the Bible, and it by no means implies any kind of automatic spiritual connection. It is an emotional device. For some, it can be a way of communicating singleness of mind.
Many of our practices, indeed, have come from pagan origins and have been justified by unrelated Biblical passages. Praying with hands held in a ring, in most applications, is one of them, and so is the superstition that merely touching a person in itself can automatically bring about some sort of "spiritual" effect. However, I think that those who prohibit the practice of holding hands during prayer for this reason miss the point.
The simple fact that a ring, for instance, is an important symbol in our pagan past does in no way prohibit us from using it to demonstrate something completely different. Pagans did a number of things holding hands in a ring, but that doesn't mean that a child will become possessed with the devil because he plays on a merry-go-round. And, the fact that pagan practices have involved holding hands should in no way prohibit us from grasping the hands of our fellow believers, to demonstrate to them that we are with them. To be wary of holding hands alone for such a reason is not only to be superstitious, but hypocritical.
But should we hold hands in a circle as if we were summoning, or standing around a pagan altar? Um, no. Should we hold hands with the belief that there is something inherently spiritual about doing so? Nope. We should simply be sound of mind and do what is appropriate.