The rationale is quite simple: They believed in an eternal Hell. Unrepentant heresy places you in eternal Hell. Hell also has levels and is not the same for everyone; not necessarily Dante's circles, but not far off. This is easily proven, just look at Saint Thomas Aquinas, who warned that sins against the deliberate intellect (heresy, blasphemy, schism) are much more inexcusable than sins of the passions and nature (lust, sloth); even if both are damnable. Vice versa, Heaven also has levels, and it was (and is) a pious opinion that no two people are ever at exactly the same level.
If Hell is eternal, and it is possible for you to make your own Hell worse, killing you if you refuse to repent directly prevents you from making your eternal punishment worse. It also prevents bringing other people with you, and the guilt you would bear for influencing other people. In a way, it is an act of charity to other people and yourself; causing some Saints and scholars to comment at the time to do otherwise would actually be hateful. There's also the issue of, if someone was going to repent, the logical assumption that going to the noose or stake is a much stronger motivator than dying in your sleep at 73.
In line with the above, the very act of burning itself was seen as somewhat of a charity. A public spectacle to warn against following them (charity to the viewers); but also a constant suggestion, even to the end, to the burned of what is waiting for them eternally, giving them one last chance to repent. For what it's worth though, Historians tell us that most of the burned died by suffocation and not by the actual burning, which would have been probably also been known at the time.
(Worth remembering, both the Reformers and the original Catholics burned at the stake for similar rationales.)