Old practices die hard. As recently as 1815 a woman was hounded to death in 'enlightened' Norfolk, England, for supposedly being a 'witch'. The local reverend even refused to bury her in the village churchyard and she was deposited under a crossroads so that the constant passage of traffic above her meant she could never achieve rest.
In the case of the Wharram Percy burials it could be that dismemberment and burning (frowned upon by the Catholic church for all regular burials) was meant to deny them an after-life. It implies they may be heretics and in Britain that normally means Lollards, a 14th/15th version of Protestantism.
https://en.wikipedia.org/wiki/Lollardy
The common medieval burial practice in Britain was that a skull and two long bones would be 'filed' in a charnel house if a body was subsequently dug-up during later burials in the churchyard. Most churchyards were small and there was great need of burial space, especially in the cities. The rest of the found bones would be dumped into an ossuary or bone store but the skull and two long bones carefully deposited in the charnel house were meant to ensure that the dead person was resurrected on 'the day'.
For this reason a skull and two long bones appears on many 17th to 19th century gravestones and tombs in Britain as a symbol of The Resurrection. This symbol was later taken over and adopted by pirates as their flag, the Jolly Roger. Whether they knew of the resurrection connection is debatable.
Destroying or damaging their bones implies the dead people were being denied an after-life as a punishment. This was a common fate for heretics and one reason why they were commonly burned at the stake. Joan of Arc is a very good example of this.
As an example of parallel thinking, North American natives often disfigured or damaged the bodies of their fallen enemies so that they would carry those injuries in the spirit world.
