(not theological ones) -- such as the confusing of holidays in Celtic Europe or the confusing of American Aboriginals by deliberately mistranslating the exquisitely poetic truth of "Great Holy Mystery" into the hierarchal/patriarchal "Great Spirit" -- and once the resultant cultural erosion was complete, savagely suppressing any doctrinal variance. Examples include the Albigensian Crusade in Southern France (c. 1200?; I've forgotten the exact dates) and the methodical destruction of the Celtic Church, which was the one genuine hybrid of Christianity and paganism. Celtic Church beliefs apparently included Mary as the most recent vessel of the Great Goddess (aka the Holy Spirit defined as female); Jesus as the most recent incarnation of the Dying God (aka Blessed Bran, Arturos etc.), "the once and future king"; Midnight Mass said in the stone circles on the moon's High Holidays: the full moons closest to February 1, May 1, August 1, and Hallowe'en (the real first days of spring, summer, fall and winter respectively); Sunrise Mass said in the stone circles on the solar feasts: the vernal and autumnal equinoxes and the summer and winter solstices, the four mid-season (Mid-spring, Mid-summer etc.) days. The Pope was so terrified by this he gave William the Bastard of Normandy full title to all the British Isles including Ireland to suppress the Celtic "heresy": the "Irish Troubles" actually date from 1066. There is persistent Scots folklore the rebellions of Wallace and the Bruce (c. 1306) were as much motivated by religious unrest as political ferment: note the excommunication of all Scots. Also, when Robert the Bruce sent his cousin Jamie Douglas aka "the Black Douglas" to burn and harry a swath through all England, he sent his brother Edward the Bruce to Ireland: by some accounts the last High King ever crowned at (pagan) Tara. Yet thanks to the Inquisition we know so little; so much of infinite value has been forever lost...
Christianity was not a borrower but a thief: the original "Indian Giver" (the very worst perversion of meaning in the entire English language, for it was the Christian whites who promised plenty but then robbed the indigenous People of everything, not the other way around as the vicious phrase implies).
To return to your specific question, what is it in Yehvehistic religion that prompts such things? I believe ultimately it is the profound theological insecurity that comes from the notion of a single lifetime judged by an ultimately unforgiving god. The mandate to conquer (the meaning of which includes the notion of imposing total obedience, total destruction) is merely a logical acting-out of the divine mandate: if "man" is made in "the image of god" as the Bible claims, then surely "man" has the right to behave as god himself behaved -- even at Sodom and Gomorrah (or toward all humans save Noah and his family as disclosed in the Flood story) -- particularly since part of the divine mandate is the forcible "conversion" of all the earth's peoples. Conquest itself is of course not unique to Yehvehistic theology: it is far older than that, (though the ecofeminist/feminist assertion that the mandate to conquer is a psychological expression singular to patriarchy is based on the ultimate truth that in the long-term sense nothing but harm can come from the Biblically ordained attempt by the sons to sell their mothers and sisters into slavery in return for immortality -- which is precisely the Biblical bargain). The archaeological evidence fully supports the feminist argument: while patriarchy (defined as male supremacy derived from the supremacy of male god{s}) has been around for only about 5000 years, artifacts from before that time all suggest a global ethos -- its variances only in local modes of expression -- in which the central figure of all belief systems was the Goddess: "the" because beyond the curtain of local language and local symbol she is everywhere the same -- the embodiment of Nature and the trinity mirrored by the moon: youth, maturity, death/resurrection. And the fact this evidence is so widespread and of such long duration suggests a truly inconceivable 25,000 or more years of relative human peace. (What ended it? We don't know: my best guess is some huge cataclysm that enabled the rebels to argue the Goddess was an unfit mother.)
Please don't imagine I am suggesting the patriarchal/polytheistic Romans who slew an estimated 90,000 Britons in the suppression of Queen Boudicca's rebellion were any more merciful than the avowedly secular Nazis at Babi Yar (whose belt-buckles nevertheless proclaimed "God is with us") or the Christian Americans at Mai Lai. Indeed they were not. What is different is not the divine mandate to conquest but rather the ultimate fulfillment of it. The Romans had the gladius, the pilum and Onager -- the finest small-arms and artillery of the ancient world. The Nazis had the Mauser, the sturmgewehr and the dread Krupp 88. The Americans had M-16s, M-60s and napalm. But only the Germans (in the nation where Christianity first became Protestant) and the Americans (where Protestantism became a global economic empire of a magnitude and economic oppressiveness hitherto unimagined) -- only the Germans and the Americans sought to use the atom, the basic building block of nature, as a weapon -- the ultimate perversion of the source of life into the source of extinction. The ultimate patriarchal/Yehvehistic alchemical triumph: the transmogrification of the ultimate embryo into the ultimate abortion -- Mother Nature at long last totally overthrown, reduced to slavery, condemned to mere whoredom. Once again, the mandate to conquest as spelled out in Genesis. Hence my argument that thermonuclear weaponry is the ultimate manifestation not just of patriarchy but of Yehvehistic theology in general: "I am the lord thy bomb and thou shalt have no other bombs before me." Alpha and Omega. The Charles Manson paradox: love defined as murder. The H-bomb as macrocosm; the suicide bomber as microcosm: "we had to destroy life to save it."
I believe that the good in people raised in Yehvehistic religion (and in patriarchy in general) survives in spite of the theology -- not because of it. I believe most humans do the very best they can: that but for the pathological exceptions (which in patriarchy seem ever more abundant), most humans are at least as considerate as wolves when it comes to kindness to their packmates. But then, like many others of my generation, I have experienced first-hand the extra-patriarchal (and therefore painfully short-lived) structures of the old Counterculture, where amid vast folly and foible I nevertheless saw the genuine human promise of the so-called "revolution in consciousness" -- the revolution that brought about not only the renaissance of feminism and the birth of environmentalism but the resurrection of the Goddess. Nevertheless I am not advocating something so ridiculous as an attempted return to the ancient matriarchy -- I think we have outgrown it, and in any case it would be impossible, for if Arlo Guthrie will allow me to borrow one of his favorite phrases, every time a tune "comes 'round on the guitar" it is at least subtly altered by its passage. What we need is not regression but progress: the advance into the Next Phase -- whatever it is that comes after patriarchy (patriarchy I believe even now is in its death throes: hence the present war) -- a new paradigm of which we can already see glimpses, even on this very thread.
For those who wonder at the sources of my analysis, here is a link to a similar discussion on another thread, complete with a rudimentary bibliography:
http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=214x23737#23845 (This is written in great haste without my customary careful editing: I have to be somewhere else too soon, but wanted to respond in detail to your questions before the evening grew old. In any case, thank you for asking. And please forgive me if my text is sometimes muddled.)