Religion has been an incredibly influential force in the world throughout history, for good or ill. While religions like Christianity, Judaism and Islam have enabled people to live richer lives and find some spiritual truth in their life experiences, these faiths have also been used to commit terrible acts. Despite these religions' ostensible focuses on compassion, life and goodness, people have used religion to cover their own misbehaviors of killing - breaking God's law while invoking it at the same time. This is a supremely unethical line of thinking, as each of these religions promotes peace, and even outside of those contexts humanist ethics decry the taking of life.
Religious wars and conflicts are common among Christianity, Islam and Judaism. Christianity in particular, during the Middle Ages, killed and persecuted many for being pagans, witches, and heretics for reasons of dubious validity (Kuper, 2009). The Crusades were a years-long war against Muslims in the Levant in order to secure the holy places surrounding and including Jerusalem; many thousands were killed in bloody conflict, all over the same piece of land (Asbridge, 2011). (That land is now the centerpiece for the continually escalating Israeli-Palestine conflict, in which Jewish and Muslim extremists kill each other in guerilla warfare.) The original Muslim conquests lasted from 634 to 750, and intermittently continued until the early 20th century; in these wars, Muslims expanded greatly throughout the Middle East, killing all non-believers in order to spread their religion as well (Fregosi, 1998.
The ethical problem with killing in the name of religion goes far beyond the unethical nature of killing someone in cold blood (i.e. not in self-defense). In all three religions, there is a fundamental understanding of God as a just and compassionate deity, necessitating communities that are kind and committed to justice just as he was (Perry, 2001). Because people are made in God's image (Genesis 1:26-17, 9:6), it follows that they should follow God's teachings and examples. One of the Mosaic commandments says "thou shalt not kill" directly (Exodus 20:13). All of these things make God an intrinsically kind creature, who wants his creations to also be good and kind. These sentiments are echoed in both Old and New Testaments, and the Qur'an stresses that Muslims must "argue nicely" to convert, even with Christians and Jews who may be perceived as worshipping the same God (16:125, 29:46, Firestone). All three of these religions, therefore, ask that nonbelievers be treated kindly, and murder is strictly forbidden, if not at least inconsistent with the attitude of their God.
In conclusion, religious-based murder and warfare is unethical and inconsistent with the teachings of God, Yahweh and Muhammed. One thing to keep in mind is that religion is hardly ever the sole reasoning behind these killings - in terms of total war, at least, there are other concerns to add. Sometimes it is a psychological need to be 'special' and 'loved' at the expense of others, sometimes people are killed for their land and property (them being of a different religion simply allowing them to justify it further). Whatever the reason, the religious aspect of it can often give people direction, or a scapegoat for their problems - this also happens in secular environments. The use of religion is disingenuous, as Christianity, Islam and Judaism alike condemn the taking of life, especially for religious conversion. As a result, it cannot be ethically endorsed in any way.
Asbridge, Thomas The Crusades: The Authoritative History of the War for the Holy Land. Ecco. 2011. Print.
Fregosi, Paul. Jihad in the West: Muslim Conquests from the 7th to the 21st Centuries. Prometheus Books. 1998. Print.
Kuper, Leo, "Theological Warrants for Genocide: Judaism, Islam, and Christianity", in Confronting genocide: Judaism, Christianity, Islam, Steven L. Jacobs (Ed.), Lexington Books, 2009, pp 3–34.
Perry, David L. "Killing in the Name of God: The Problem of Holy War." Santa Clara University. 2001.Lecture.