I assume that what you are referring to are some of the laws encountered in the Old Testament, which were part of a legal structure designed to apply to the Israelite nation (and no one else, point of interest). From a Judaism perspective, the law is supposed to apply only to Jews - those who are part of the religion and the race.

Yes, because murder and genocide make perfect sense as long as you restrict them to a particular place and time! And there are such things as "races" and it makes sense for them to be units of moral analysis. And obviously "she must marry her rapist" (Deuteronomy 22:28-29) is a totally sensible rule for an ancient culture, and neither the Greeks nor the Chinese had figured out anything even remotely better by that time period. Yes, obviously, it was totally fair for Moses to be talking about slaughtering the Amalekites (and their children, and their cattle; Deuteronomy 20:16-17) at the same time in history when Demosthenes and Epicurus were debating about the proper form of democratic government. And no one today takes those ideas seriously, and certainly there aren't millions of Americans who use passages from Leviticus (18:22 and 20:13) to argue against gay marriage.

And of course Jesus came to change the rules; that's why he put it so plainly in Matthew 5:17-19:

Think not that I am come to destroy the law, or the prophets: I am not come to destroy, but to fulfil. For verily I say unto you, Till heaven and earth pass, one jot or one tittle shall in no wise pass from the law, till all be fulfilled. Whosoever therefore shall break one of these least commandments, and shall teach men so, he shall be called the least in the kingdom of heaven: but whosoever shall do and teach them, the same shall be called great in the kingdom of heaven.

\end{sarcasm}

Witness what religion does to a human mind; it makes an otherwise intelligent and reasonable person defend the obviously indefensible, because they cannot bear to accept the obvious fact that what they were told isn't true. Suddenly genocide becomes "a different time" and rape becomes "their culture", because the thought that so many people's precious beliefs are false is simply too much to bear. Contradictions in holy books are somehow seen as a good thing, because they let you take whatever meaning you want and declare the result infallible (when it's obvious from basic logic that contradictions in beliefs are always bad).

Of course no religion is harmless. Delusions are never a good thing. Some religions are more harmful than others, I'll grant you that; but if you want to know why Islam is particularly bad, it's because it actually follows the book. Jews and Christians have largely given up on the crazy evil books, and so they can behave (mostly) like reasonable human beings. Muslims haven't, and that's why they do things like hang gay people and keep women covered head to toe. Confucians are an interesting case, in that their books contain falsehoods, but are not genocidally insane, so that counts for something. Jain are also crazy, but crazy in a way that makes them relatively harmless---like the Amish. So if I could make every Muslim in the world suddenly turn Jain, I would; but I'd rather turn them atheist. What's more, I find it's easier to make people atheist, because the rational part of their brains already wants to.

As for what evil means, no, it has nothing to do with religion (other than the obvious fact that religion makes assertions about it, just as religion makes unfounded assertions about literally everything). Evil is found in human suffering, particularly when it could be easily prevented. It is found in death and destruction, especially when we are in a position to avoid them. Am I a utilitarian? Yes, I suppose I am---if you are not, you must be saying that your decisions can't be made to fit a Von Neumann-Morgenstern decision utility... and isn't that a lot like saying your decisions are irrational? If you meant to say that human beings rarely engage in intentional evil (accidental and negligent evil is far more common), that's actually a very good point; but then, this is just one more problem with religion, because religion often asserts that our enemies are servants of demons whose only goals are pure evil.

The net amount of human suffering would be decreased if people abandoned religion altogether. If they continued to believe in religion and stopped being hypocrites, no... I stand by my previous claim. They would burn people like me and most of the rest of Less Wrong at the stake. The war between Catholics and Protestants in Ireland would flare up once again, and really if theology is as important as people say, even Baptists and Methodists should be torturing each other over doctrinal differences. It is only a lack of religious fervor that defends civilization as we know it; and if given the choice between fanaticism and hypocrisy I wholemindedly express my preference for hypocrisy.