To question it as a cultural problem, where was there ever a non-problematic Judeo-Christian presence? And most importantly, what is or has happened to be the most problematic, more or less strict?
I don't mean to take this out of context, but certainly you wouldn't blame the Jews for the Holocaust or other persecutions (against either Jews or Christians). The problems can start from any party, so I'd hate to shift the blame just to the religious parties. You can be a radical atheist/christian/jew/muslim/communist/etc.
Where was Judeo-christianity ever integrated? Where was it ever reformed peacefully. Are there not enough examples of implementation? Or are they now outdated? What is the timeframe where to those it has been extremely lethal, you can safely and convincingly say that it is now in the past?
If everyone had the same beliefs, then great, there wouldn't be conflict because of those beliefs. (though there would certainly be conflict about other things, resolved peacefully and with respect or not...) But we should definitely consider how each belief system treats non-believers and apostates, because those ethics are important for humans to function well as a multicultural society (if that is indeed what we want to see come to pass -- do atheists want all non-atheists to become atheists?). Sometimes the practice of some religious group is different than the theory (i.e. the books and teachings it holds sacred), too. By what standard should we judge?
But like you mentioned (I think you said something along these lines), it's hard to make judgments on these things as if we're outside of the system, since we're a part of the whole, too. Our judgments of other belief systems change the way we treat "non-believers" of our standard/beliefs. Do we pity them? Do we belittle or revile them? Do we have compassion for them?