Let's take a look at the harm it has done. Thirty Years' War: Protestants vs Catholics (3-11 million casualties). French Wars of Religion: Protestants vs Catholics (2-4 million deaths). Nigerian Civil War: Islam vs Christianity (1-3 million deaths). Second Sudanese Civil War: Islam vs Christianity (1-2M dead). The Crusades: Islam vs Christianity (1-3M dead).
Religion tends to be the last to support equality. The KKK is a Christian organization wanting to base rights on skin color. Islam and Christianity don't support rights for homosexual couples. Christianity and Islam discriminate and suppress women.
The wars:
War is a part of human history, people enjoy killing each other, taking each other's stuff and conquering. the religious wars you named (and i'm surprised you didn't mention the inquisition, which enjoyed frequent heretic burnings) would likely have happened over other differences in beliefs or desire for territory regardless of the existence of religion. In many cases it was just one country wanting another's territory (happens all the time for non-religious purposes) or someone wanting more rights or freedom (protestant vs catholics, too many examples that do not involve religion for me to name).
Disagreements in opinions result in war because humans are stupid, petty, intolerant creatures, the fact that a few of these were caused by religion doesn't mean that religion is the worst possible thing to come to mankind- it just proves that mankind is intolerant of other people.
Religion was merely man's excuse to be brutal and violent, not the cause.
As for the KKK:
You have to realize that Christianity contains, what, a billion? More followers? You take a billion people and examine each and every one of them, you'll find a hell of a lot of fucking assholes. The KKK are a white supremacy group that tries and hangs on to religion in order to draw in more supporters, but that doesn't mean they are acting with the approval of religion in itself. Just because something is done in the name of god, does not mean that the god in question or his followers would approve of it (If you have a stalker who is obsessed with you, and he cuts off animal genitalia and mails them to you in admiration, it doesn't mean you like it, pretty much the same thing with the KKK). (I think that if there is a god, he would be shaking his head at all of us, and then just annihilate the world out of exasperation and start over)
The KKK is an extremely small percentage of the total christian population, and it was formed in a country in a time that was noted for it's extreme racism. it's a minority, and not a well liked one, it is not an accurate depiction of most of them.
As for women, keep in mind that religion was formed in a time where men dominated women (and no, not in the hot way), and sexism was rampant, it would naturally influence the religious beliefs of the time. Now, you might argue that religion is something that should have changed with time to fit new cultural beliefs and tolerance, but I believe that would defeat the purpose of the religion in the first place.
Religion cannot be blamed for the flaws it presents, that's just how shit was back then. People made the religion agree with the typical cultural beliefs in order to draw in more followers.