To modern sensibility, decapation seems a shocking and barbaric means of execution. We are much more comfortable, as it were, with "lethal injection" or even gunshot wounds--the illusion of speed, lack of pain, and lack of brute force that make taking the life of another person appear "civilized."
In the Middle Ages and early modern era, on the other hand, beheading was considered too swift and lenient for heretics. That's right--it was the merciful execution.
For relapsed heretics in the late Middle Ages, that is, convicted heretics who initially recanted (sparing their lives) but then returned to "heresy", the ideal punishment was burning at the stake. This was in part spectacle, in part making the death fit the crime, but also meant to destroy the person's body (a) beyond hope of bodily resurrection at the Day of Judgment (b) to prevent any followers from gathering bones or clothing to venerate as saintly relics.
This view persisted into the violent upheaval of the Reformation era, when Catholics burned Protestants, Protestants burned Catholics, and everyone burned Anabaptists. But there were signs of growing discomfort with the visible brutality of burning people alive. Not for the heretics themselves, you understand--for the sensibility of people who watched. Frequently, women were sentenced to die by drowning instead of burning (Anabaptist theologian Balthasar Hubmaier was arrested with his wife Elisabeth. He was burned; she was drowned). But make no mistake, drowning was not considered an easy death--being staked through the heart was judged more merciful, according to Joel Harrington in Faithful Executioner. What it was, instead, was less gory for viewers. As Harrington points out, beheading was considered the most actually-merciful for the condemned of all.