Although we must respect other cultures, but also we must revolutionize said cultures and do away with all of the oppressive social relations that exist or may re-emerge in this process(including communists). The simple fact is that these stories in the Bible and in the Qur'an are reflections of ancient societies, and also reflect those same productive and social relations, ideas, and class distinctions, which are a stigma on humanity and development. Taking the Bible, or the Qur'an, literally is a horror, and it keeps people from engaging with reality with a scientific approach, a truthful understanding.
In a revolutionary society(Maoist), people will continue to have the right to worship, but they will have to come to grips with the fact that all gods are a myth(and thank god that is the case! lol). People's religiosity will wither away as the need for an escape to their suffering will wither away. But right now, all atheists, whether or not communist, should be confronting and openly engaging with people that are religious, but in a polite way, and not put people down or "slam" them for their religiosity. But in a way that may make people uncomfortable, may even offend people. That is the dialectic we are faced with.

btw, Islam is not the only religion that has caused great human suffering, let's look at what the Christians have done, and are doing--and trying to do now. All religions, in the fundamentalists, have committed horrific crimes.