In the course of discussing Marriage Equality here, we have entered into what I see as a two-headed discussion of the Church's role in society in general. I think the two heads of the discussion are has Christianity been a net good in society and can Christianity be a net good in society. Notice the issue is net good. It would be impossible to argue that Christianity, or any organized religion, has not been a force for good and evil in society. Indeed, I would suggest a significant force for good and evil at times.
My meta question is this: Is it possible to evaluate the effect of a society's predominate religion independent of other cultural elements of a society?
Addressing the historical question, Atrios put it this way, asking about religion's effect on history is like asking about the effect of weather on history.