Even if Orthodoxy did lead people to Atheism, it wouldn't particularly bother me. Let's just assume for a moment that Orthodoxy is the only religion that is acceptable to God and Atheism is a rejection of the existence of a deity. Now, you could take the easy way out and choose another religion (such as the Protestant heresy) but for most people, that isn't good enough. For me, it really is between Orthodoxy and Atheism.
I live in a Muslim country, and thankfully in the past few years, I have spent so much time studying various religions of the world. Within my family, I have no doubts that I am the most knowledgeable about various religions. The ones I am most well versed on are Islam (most Shia, but some Sunni as well), Hinduism, Baha'i, Sikhism, Judaism, and various forms of Christianity (Orthodoxy, Catholicism, Mormonism, and several varieties of Protestantism -- definitely not all of them of course). I have knowledge of others as well, but these are the main ones I can safely say I have a high level of knowledge about. Now, to get onto my point. I have no doubts that if a God exists, Orthodoxy is his religion. My family is Protestant Christian. I grew up in various Christian churches (mostly meeting in peoples houses because there aren't too many Churches here -- but a lot more are being built thanks to the fall of Saddam and the introduction of democracy) and I spent 4 and a half years as a Muslim. Throughout all of this, I was searching for God. I have finally found him. I could write entire books on the reasons I reject the other religions I have studied, but it's not particularly important.
Orthodoxy is the true representation of the New Testament Church. And thanks to Biblical archaeology, we can be sure that the New Testament is preserved as it was written. So unless the Church Fathers were liars and fabricators, we can be sure that what is written in the New Testament is true. Therefore, we can conclude that the Orthodox Church, as it is known today, is the Church that Christ founded nearly 2,000 years ago. Now, let's assume for a minute that any converts to Orthodoxy (as well as many people that were raised Orthodox, however not all of them) are aware of this. They know that Orthodoxy is the true representation of Christ's Church. They also know that Christ claimed to be the Messiah and the Son of God. So unless they decide to completely reject Jesus and go to some other religion that doesn't accept Jesus but still believes in God (Judaism, Hinduism, Sikhism, etc.), the choice is simple. Orthodoxy or Atheism. If God exists, Orthodoxy is his religion. If God does not exist, then Atheists are correct in rejecting him.
The reason that I would not be bothered if Orthodoxy led people to Atheism is because at the very least, it makes a person think. If somebody knew the truth and through personal study and dedication decided that he does not believe that a deity exists, I would have a much higher level of respect for that person than somebody that accepts or rejects anything without truly understanding both sides. To me, Atheism and other religions are all the same. They are (respectfully) in the hellfire. To say that Orthodoxy leads to Atheism would be like saying that Orthodoxy can lead to anything since all it takes is for somebody to convert to another religion.