War in Islam

I regret to say my friend has refused permission for his mails to be published in this blog. I hope that this will not make it too difficult to follow the arguments that follow. 
I am enclosing a short rebuttal to the first half your last long mail before I forget. My main concerns this time around are mainly political, as you will see. But there are other issues, especially with the ahadith, which I would like you to clarify for me. You kindly directed me to a site ( a "traditional, scholarly site" - I think you referred to it as) in response to a request and I came across this very clear definition of the reliability of Bukhaari (spelling seems to differ):  “Among the ahaadeeth which are attributed to the Prophet (peace and blessings of Allaah be upon him), there are some which are saheeh (sound), concerning which there is no doubt that they are the words of the Prophet ... Books of saheeh have been compiled which include saheeh ahaadeeth such as Saheeh al-Bukhaari and Saheeh Muslim” Fatwa number 11443 http://www.islam-qa.com/en/ref/11443 .
Is this something which you accept?

Now to my answer...

When you meet the unbelievers, strike off their heads; then when you have made wide slaughter among them, carefully tie up the remaining captives – Qur’an - Surah 47 verse 4.

Kevin explains that this verse was revealed after several years during which fighting the pagans was prohibited. God is now giving the Muslims permission to fight the unbelievers. He finally asks if I would agree that rules on how to fight war, including on how to kill the enemy, should be included in any code of laws that purports to be complete. Obviously I agree that we need rules to govern warfare. To that end we have the Geneva Conventions and Protocols which, I would suggest, give more useful and detailed instructions on the subject than “beheading”, “slaughtering” and “tying up captives”. To claim that this gruesome exhortation is part of a set of sensible guidelines for the humanitarian waging of war, strikes me as bizarre... to say the least.
In any case, Islam is far from clear in its prohibitions. Does Islam really make it clear that women and children are to be spared in war, as you have previously claimed? This hadith, from  Bukhaari, suggests otherwise:
Bukhaari:V4B52N256 "The Prophet passed by and was asked whether it was permissible to attack infidels at night with the probability of exposing their women and children to danger. The Prophet replied, ‘Their women and children are from them.'"
(Again, I ask you: If the Prophet is supposed to be a perfect example to us (as Allah claims), and if his sayings and actions are supposed to guide us, how are we supposed to reconcile such clearly conflicting advice?)
 I do, however, agree that there are plenty of surahs dealing with the topic of war.  Can you explain how the following should be used as guidelines?...

Your Lord inspired the angels with the message: 'I am with you. Give firmness to the Believers. I will terrorize the unbelievers. Therefore smite them on their necks and every joint and incapacitate them. Strike off their heads and cut off each of their fingers and toes”. 8:12     “Allah wished to confirm the truth by His words: 'Wipe the infidels out to the last” 8:17    “The punishment for those who wage war against Allah and His Messenger and strive after corruption, making mischief in the land  is murder, execution, crucifixion, the cutting off of hands and feet on opposite sides, or they should be imprisoned.” 5:33 
Perhaps we should suggest the lopping off of fingers and toes be added to the Geneva Protocol...not as a proscription... but as a prescription. (Or have I misunderstood the gist of the Almighty’s advice?)
And as for your argument that Islamic rules help us to avoid atrocities or “ drawn out” deaths/punishments, can you explain Mohammad’s vile torturing to death of the apostates and criminals in this hadith (again from the reliable Bukhari)?
Narrated Anas: Some people . . . came to the Prophet and embraced Islam . . . [T]hey turned renegades (reverted from Islam) and killed the shepherd of the camels and took the camels away . . . The Prophet ordered that their hands and legs should be cut off and their eyes should be branded with heated pieces of iron, and that their cut hands and legs should not be cauterized, till they died. (Bukhari, Punishments, no. 6802)
I appreciate that you will no doubt accuse me of systematically picking out verses that show Islam in the worst possible light and of not taking into account the context. You will perhaps say that I have approached Islam from a too critical standpoint and that I should be more open-minded. I would counter that if one is to contemplate adopting a belief system, then one owes it to oneself and to one’s family to find out as much as possible in an objective a manner as possible. I would also counter that there are so many examples of Mohammad’s cruel behaviour in the ahadith that it is difficult, to say the least, to see him as a perfect human. Indeed, as I am sure you are aware (and if you aren’t, you need to be) Hisham, the first editor of Mohammad’s first and most respected biographer, Ishaq, admitted that he edited his work to avoid showing the Prophet in a bad light:
“I have omitted things which are disgraceful to discuss, matters which would distress certain people...”
Given the distressing accounts of Mohammad’s assassinations, slaughtering, ethnic cleansing, pillage etc. etc. that  Ishaq was apparently happy to include, one wonders what horrors were omitted.
I have read a great deal now. I occasionally come across a verse, or detail from the Prophet’s life, that makes me think that here is a belief system that has something positive to give to humanity. But more often than not, I am left confused and concerned that you should have devoted your life to such a religion. Moreover, when I visit Islamic sites in an attempt to gain an insight into why people follow the faith - to genuinely try to understand - I am left flabbergasted at the desperation of the writers to convince people of the miraculous nature of the Qur’an and ahadith.