They're compatible and contradictory at times. One of the most effective purposes of religion is to explain what what science can't, or won't.
Regardless, I think the premise of this story is invalid. He seems to use the argument: "Well, he must have done something to deserve crucifixion" as the cornerstone for his piece.
Seems to me that justice and injustice are doled out disproportionately, unevenly, unpurposefully all the time. Why would Jesus' crucifixion have to result from a just sentence?