The thing about the Koran is that if I read it right you could defend a very wide variety of stances depending on your strategic position at the time.
The Muslim scholars through the centuries have headed off that approach by stating if there is any conflict while reading the Koran go by the later chapters which supercede the earlier chapters in the Koran.
The later chapters are more violent, and Muhammed sets the example of how to deal with non-believers in the Hadiths. -Tom