$1:
Well an atheist treating it as a holy book would be an oxymoron. It's not like they pray over it, use it to swear oaths etc. That's the diff.
Why? Atheism is a broad belief set, but generally ties into the belief that there is no god, not to rejection of spirituality as a whole -- that implies apatheism or other such branches within the greater atheism umbrella. Secular religion and other concepts which encapsulate such things as Communist or Free Market beliefs all have books which, while not containing divine preachings, do contain key phrases or beliefs which are commonly repeated amongst atheist or agnostic followers.
Generally, saying that the difference between a holy book and other books is that people swear and pray by one is too narrow. They are books which are often considered to be supernaturally inspired and as such are sacred, or are writings which contain central points of that movement. While not supernaturally inspired, The Communist Manifesto and the Little Red Book both could fit into this description, as could others. Just because atheists do not believe in a god, however, does not mean they automatically switch over to following sound scientific methodology specifically for all actions, and hence consider such a book a key center to their belief system since it relates to the theory of evolution which played a role in expanding research in that direction. Hence, while I'll agree the use of that book in the context provided is flawed I don't think the definition you used for holy book directly encapsulated the entirety of atheism and hence fell by the wayside to be considered an oxymoron. That's just me though.
In short, a largely irrelevant ramble from an agnostic playing Devil's Advocate. The Qu'ran debate has quickly become one of repetition I think anyways, with the same rotation of comment and counter-comment going on for a few threads now. Hopefully people don't mind me turning that nice round O into a Q for a short moment.
