You should always question any book, especially religious books. No one is telling you not to question the Islamic scriptures, just to take them in context.
There is no need to bring in other scriptures "to contradict" the verses that you listed. Your understanding of them is what is the issue, not the scripture itself. You seem unable to wrap your head around that point.
The scripture that you brought up was no different than the story of the Hebrews taking the city of Ai in the Bible. It's really that simple - and not really controversial. It was written about a battle in which a few Muslims defeated a much larger force, and killed all of the non-believer leaders. Read all 75 verses of Surah Al-Anfal - not just one. Read up on the Battle of Badr, which the surah was written about: http://en.wikipedia.org/wiki/Battle_of_Badr - prior to this battle, the Muslims had no established moral principals. You blast them on their morals, and you blast this surah, but that is exactly what it was written to help start to establish.
The surah is really about:
- The fact that the victory was due to the help of Allah rather than their own efforts and bravery was stressed so that Muslims should learn to rely on Allah and obey.
- The moral lesson of the conflict between the truth and falsehood was explained.
- The mushrikin, the hypocrites, the Jews, and the prisoners of war are addressed advising them to learn a lesson.
- Instructions to the spoils of war. Muslims were told not to regard these as their right but as a bounty from Allah. Accept with thanks the share that is granted to them out of it and accede to the share which Allah sets aside for his cause, and for the help of the needy.
- Normal instructions concerning the laws of peace and war, needed at the stage which the Islamic movement had entered. It enjoined that the Muslims should refrain from ignorance whether they are in peace or in war and establish moral superiority in the world.
- The differences of status of Muslims living within the limits of Dar-ul-Islam, from that of the Muslims living beyond its limits.