The great multitude (by the most conservative estimates over twenty million) of the New Martyrs and Confessors of Russia who suffered for their Orthodox Faith in our Lord and Saviour Jesus Christ, testify of the extreme militant efforts the atheist enemies of God had to resort to in their attempt to inculcate their false beliefs on the populace.- http://www.orthodoxinfo.com/praxis/infoage.aspx
Most Christian groups(such as the Catholic church, for example), view atheism as more of a spiritual disease, brought on by apathy and pride. Of course, these views are also largely mirrored by other religions, such as Islam and Judaism.
Neither of these views are consistent with atheism as I experience it. Since my experience is generally congruent with those of most atheists I know, I do not think I am anything of an anomaly. My atheism is built upon one principal: everything I think I know or experience is open to critical analysis. In other words, there are no sacred cows. There are no questions which should not be asked. This includes the big questions, like the existence of the God.
Religious writers make many mistakes when trying to analyze atheism. A prime one is an attempt to redefine atheism to suit theistic terms. To take an Eastern Orthodox quote as an example:
Atheism is the assertion that there is no God. Atheism is itself a belief, since to know that there is no God is impossible. Thus, Atheism is faith that there is no God, a faith in an un-God. - http://www.orthodoxinfo.com/praxis/infoage.aspx
This is simply not true. Atheism is a lack of theism. Anyone who does not assert a theistic belief is a de facto atheist, whether they actively deny the existence of God or not. Atheism is not the addition of an anti-God philosophy, it is the lack of any theistic philosophy. Many theists attempt to assert the above claim in order to portray atheism as simply another brand of religion.
Aside from the false generalizations, I think the Eastern Orthodox have another problem in approaching atheism: the tendency towards mystery. They have a tendency to wrap their theology in mystery(to the point that 'mystery' and 'sacrament' can be interchanged). All Christian groups have this tendency in some measure, but the Eastern Orthodox are especially affected by it. Of course, this is in direct contradiction to skepticism. An inquiring skeptic is not satisfied with fencing off some ideas and avoiding analysis.
This combination of factors makes discussing religion with Eastern Orthodox apologists a challenge. There is very little common ground to start. Keeping the above in mind may prove fruitful.