Good question.
I think we could all agree that a huge list could be developed for both points, one list showing the ways religion has caused harm, and another showing the ways religion has caused good. Juggernaut already pointed out some examples of religion doing harm.
But the crucial question is whether it is religion that is causing all these bad things, or whether it is people that use religion to do bad things. If it is the latter, is religion to blame? But first off, what is religion? Because to blame “religion” for bad things we must first know what it is. Presumbably a group of people that experienced the divine in a certian way, then wrote it down, codified it, and usually have a moral code, etc. What are the basic values of religion? What is the fundamental moral code of religion? Well, if you actually read, look into, and ask practicioners, you will find that all religions seem to preach good things, like universal love and compassion. None of them (that I know of) have hatred, or anger, or violence, or lying, or stealing, as their core values. (I’m talking in theory here, not practice.)
For example,
No man is a true believer unless he desires for his brother that which he desires for himself. Islam
Comparing others with oneself, one should neither strike nor cause to strike. Buddhism
One hsould never do that to another which one regards as injurious to one’s own self. Hinduism
Regard others’ gains as if they were your own, and their losses in the same way. Taoism
Do not do to others waht you would not like yourself. Confucianism.
And on…
How could people take these basic principles, which are at the core of religions’ moral codes, and cause harm in the world? Well, they do, of course; but is that becasue religion is bad, or people are bad and use religion for their own purposes? still, one cannot help but notice all the wars that were clearly done in teh name of religion, which makes me wonder if humanity is even ready for religion (assuming that it is good). If religion is good, how can we mess it up so bad?
At any rate, my view is that a any particular church will more likely do much more good for people and the surrounding community than I will ever do in my life. When it comes to morality and religion, I think that theoretically they can be separated (like Kant’s theory of morality), but in practice they are not. Besides my family, religion has been the only “moral” influence on my life. Well, and philosophy, but most philosophers nowadays are not teaching people to be good people; they just like to talk about morality.