The only aspect of this that I am not was covered, is how Islam teaches to read the Koran, specifically in cases of conflicting passages. If two passages conflict in message, the later scripture overrides, or abrogates the earlier scripture passage.
The problem here is that Muhammad wrote throughout his life in what became the Koran. If you follow his life, he started in Mecca and was professing a peaceful message. He left in 622 and traveled to Medina. In Medina he turned towards war and violence, and his scripture writings reflected his actions. After conquering in Medina, he and his followers returned to Mecca and conquered there as well.
As a result, the violent and later written scripture passages abrogate the earlier and peaceful written scripture passages. I wrote a paper in college on Islam, and I have yet to find anything that disagrees with this information but am not professing to be an expect or that I am even correct.
Here is more information with examples.