Please explain why the same sorts of atrocities appear among diverse cultures that share that particular religion. That is the main question in all this. How can one claim that it is not the religion that leads to the atrocities?
Most of these atrocities can be found outside of the religion as well. If we look at blasphemy for instance, we see a similar idea in Christianity (the Inquisition and witch hunts for example). We also see it in non-religious aspects, such as the Red Scare. So we do see such atrocities regardless of religion.
If these events were happening in just those religions, it would be easy to state that it was an aspect of that religion. However, when we see these events occurring in a wide range of ideas, the it really isn't possible to blame on religion or religion at all (that is if they also occur outside of religion).
Further, in many cases, it is clerics who are howling for blood. One would assume that those clerics are expert in their religion.
There are many clerics who are simply corrupt. They want power, and absolute power. You get that by ruling with a strong arm. And in fact, we have seen that throughout history in those areas. The various tribal leaders ruled in a similar fashion. We have even seen brutal dictators doing the same thing as well. It is nothing more than ruling with an iron fist.
It may be that, although the holy texts may not explicitly call for the atrocities, they may induce attitudes that lead to the atrocities.
One can misconstrue the texts to defend the atrocities. It actually isn't hard to justify anything with a holy text. Partially that is because they are such massive works, created over a long period of time, in many different situations.
However, when we see the vast majority of adherents not interpreting the texts in those ways, then it is pretty safe to bet the extremists really are misconstruing the actual text.