This is the best attempt I have seen to argue for a disconnection between these, while using the history of religious violence against religion.
Without a doubt, the crimes of professed communist regimes were terrible. But it is important not to lose sight of what caused them. This is the first major misconception: that the communists attempted to understand the world through reason and science rather than faith, and that this was the error that caused the crimes they committed. Communism was categorically not a reason- or evidence-based view of the world. Quite the contrary, it was a dogmatic, anti-rational ideology every bit the equal of fundamentalist religion, where certain propositions were taken on faith and were not allowed to be debated or questioned. Although the communists congratulated themselves for their liberation from superstitious thinking, in reality they had not escaped dogma; they had merely transferred their dogmatic beliefs from the tenets of religion to an equally rigid and inflexible set of political beliefs.
Read more: http://www.patheos.com/blogs/daylightatheism/essays/red-crimes/#ixzz3YkceohnH
But doesn't this presuppose that if you remain evidence-based, you will always be able to persuade others. But what if you can't, and you think it's really important that people accept the results of you reasoning if they don't reason their way into it themselves. And you have the power of the sword in your hands.