You have brought up some excellent points as well, particularly emphazising that modern atheism is "an outcome of situations prevalent in western Christian society". I think that's the key there...the society. While the religion of western Europe most certainly had much to do with the shaping of the society, many other factors did as well. The society as a whole, I believe, was not prepared for the sudden appearance of the writings of the ancient Greek philosophers. These ideas must have seemed strange indeed from the viewpoint of a 15th century university student, who was among the first people of Western Europe to read the ideas of, say, Epicurus in one thousand years.
However, I think it is fallacy to isolate "western Christianity" as the "root cause" of humanism and its progeny deism, agnosticism and atheism. As Dan Lauffer pointed out a few days ago, the Church did its darndest to combat these philosophies. However, thanks the medieval and feudal baggage the Church had burdened itself with, the words from the pulpit went unheeded. One of the few things keeping traditional Christian philosophy at the forefront was the monarchial institutions of Western Europe. There were self avowed Deists and Atheists and Agnostics in Europe, but they were very much the fringe. All that changed with the success of the American Revolution, led by, as you pointed out, a number of Deists. The Monarch, put in place by Divine Right, became supplanted for the State. And, admittedly, jumping ahead, we have, less than a hundred years later, the State being supplanted for God via Marxism.
I guess my point is that while Western christianity, through its use of rigorous scholasticism, had a PART to play in the emergence of atheism, it alone cannot be held responsible for it. A number of factors, from economics to nation building politics, led to the rise of atheism and the ultimate proclamation of the State as God.