Sorry I haven't jumped in earlier, but I've been struggling with reading this book. It is not that I find his arguments incomprehensible (which I don't) but that I find his attitude and arrogance very offending. As N.G. pointed out, Dawkins repeatedly sets up straw men to attack after saying he won't. He belittles those he disagrees with rather than allowing for honest differences of opinion. He claims that religious defenders misinterpret quotes from respected individuals, but then claims insider understandings of the respected individuals and their quotes without much more than his own say-so as to what makes his understanding better than that of others.
When I've been reading this book I find myself feeling like I do when I take some of the ridiculous surveys on the internet about "which [choose your category] are you?" The questions which are asked as multiple choice don't give choices which match my own feelings/beliefs/understanding/whatever. When he sets up a dichotomy of belief or disbelief he narrows the question so much that if pressed I would have to agree with him most of the time that I cannot believe the straw man he's knocking down, but since it is just a straw man and not really relevant to my own struggles for understanding I don't feel like I'm getting much from him.
I guess it is helping me to better understand some of the arguments people have made over the centuries, but I don't usually go back multiple centuries for insights about my modern (or is it post-modern) beliefs about the nature of God and Jesus and what it means to me. I find I agree with a lot of John Spong's writings and often feel inspired by them, but I don't usually go back to Jefferson, Constantine, etc. as sources for how I view God and religion.
I like your reference to the survey about scientists who acknowledge at least spiritual leanings. I think a lot of this gets back to the survey methodology. I don't think the shift in ten years is as much a change in attitude as a difference is question. If an atheist trying to show that scientists are not religious asks the type of straw man questions Dawkins uses then I don't doubt that it would show that most are not religious. If, on the other hand, a survey was trying to find out if scientists felt there was value in spirituality, meditation, religious customs and traditions, or other more general attitudes associated with religious beliefs then it would not surprise me to find that one or more such things are important to large numbers of scientists.
I did have one point in particular in your post which I wanted to ask about.
Do you have any references for this? It is clear that there was disagreement among early Christians just as there continues to be today. However, I am not aware of reports that early Christians persecuted other Christians until after the co-opting of Christianity by Rome and Constantine. It has been my understanding that even the idea of heresy wasn't around before this establishment of official recognition of the church by Rome.