The Holy Quran has NO general instruction to kill. If this were the case, why don't Muslims kill every foreigner in their country as soon as they step on Muslim soil?
The fact of the matter is the verses in the Quran describe war between those killing Muslims because they were Muslim.
Muslims were told to defend their themselves. The history of Islam is marked by the Hijra, The Pilgrimage made by Prophet Muhammad to Medina from Mecca to escape death by the Meccans.
The Meccans pursued the Muslims to Medina and this is when the Muslims were commanded to defend themselves.
They were persecuted for 13 years in Mecca for no reason other than that they were Muslims. They endured this persecution without lifting an arm.
The war of Islam is and has always been a defensive war against those who do not allow them to practice their religion or who fight them because they are Muslim.
The Old Testament verses ARE a general instruction to kil as women, old people and children were all killed. Did babies worship heathen gods?
Islam does not allow for killing women, old people or children or damaging trees. There are several laws on conduct of war. Salahudeen was a good example to the West of Islamic behavior during war. Of course, the best example was the Holy Prophet Muhammad (peace be upon him) himself.