While there certainly is something to your observations, I can't help but wonder if there were other motivators involved in these stories.
Middle-Eastern terrorists are often motivated to do anything that goes against Western thinking (Christian or not). So this could have been a motivation for committing these acts.
Scientists are often motivated by money and fame. What scientist doesn't want to be the one to discover the cure for cancer?
So, maybe the newspaper was unable to verify actual driving force behind these stories, so instead of conjecture, they just reported what happened and left it at that.
Not that I'm arguing with your points..... I agree that there certainly is something more to the stories than the media reported. I'm just offering up another alternative.