If you take it in the context in which it was written, the world was very different and much "smaller". At that point in time, there was little distinction between what constituted a citizen or a soldier. It was considered "normal" for a group conquering another to kill/execute the male citizens back in those times, in that part of the world - and that was not limited to the Muslim/Jewish conflicts. All of Europe, and most of Asia also had these violent tendencies in their cultures as well. The decapitations/executions and severing of limbs was not unusual at that point in history.
When you say that religion is declaring war, it shows that you do not understand the history of the book or the region of which you discuss.
There were two groups - those that followed Mohammed, and believed in his words, and those that did not. Those that did not were "non-believers" obviously, and did not try to live peacefully with Mohammed's followers, so of course, they were the enemy. The actual writings were not made until around 150 years after the death of Mohammed, from what I have read. Up until that time, they were passed down orally from generation to generation.