First off, there are two events that are being talked about in this sentence.
- Wycliffe died.
- The Pope (was so infuriated that he) ordered the bones to be dug up....
We generally use the past participle to refer to an event that occurred before another event. Note that both these events belong to the past. Keeping this in mind, a sensible way of putting together the two ideas would be
The Pope was so infuriated by his teachings and his translation of the Bible into English that 44 years after Wycliffe had died, he ordered the bones to be dug-up, crushed and scattered in the river.
We are referring to two events that took place at a definite time in the past. In such a case, the simple past can be used as an equally good alternative to the past perfect tense. This helps because we've already explicity mentioned what happened first, through the use of after. The primary purpose of using the past perfect is to bring out the chronology in the ideas being expressed in the sentence but it can be avoided in cases where it can be automatically understood.
Therefore this is also right.
The Pope was so infuriated by his teachings and his translation of the Bible into English that 44 years after Wycliffe died, he ordered the bones to be dug-up, crushed and scattered in the river.