My sense is that this type of study is often fueled by the idea that religion itself is the corrupting factor in terms of violence - it has its own bias from that premise onwards.
But, even if the methodology is sound, the entire premise that religion promotes one specific idea (either "good" or "bad") is bullshit; this is a modern obsession and interpretation of what a religion should be like. It is an idea that does not hold up to the evidence of history, as religion is and always has been a complex system of ideas that shift and adjust with every culture and historical circumstances. To reduce it to such bipolar categories (good/bad, black/white) is intellectual laziness.
You cannot separate religious ideas from the general culture.
Accurately defining the nature and practice of each religion, and whether or not it actually promotes one behaviour OVER that of another behaviour is impossible. For example, the whole idea of a "forgiving god" is a Western one. Other places in the world have no such concept, and they are not more or less violent than we are.
Even the secular worldview is right now brewing its own schisms and disagreements in the flame-war blogosphere; give it a few hundred years and it will be EXACTLY the same as religious worldview, i.e. warring and fighting about how to define the principles they attach to the notions of secularism.
People will always - ALWAYS - find ways to divide themselves by in-group vs out-group dynamics, and then find ways of expressing those divisions violently. It's the nature of humanity itself. Our particular worldviews simply amplify and motivate us to express our basic tendencies.